I didn't really see a compilation of these stats anywhere, but I thought it would be a useful reference to people.
While sales aren't everything, I'm sure that Sakurai and Nintendo consider them. Beyond the polls of Smash fans, sales are also an indicator of who is popular, recognized and so forth among fans, including the less hardcore. I'd guess that they're more important when a series still has major cast members left out (as with DKC or Metroid). Zelda has its most important characters included, other possibilities would mostly be characters that only appeared in one or two games or are quite minor, so I think the sales is less important at this point. But if Ganon wasn't in, we'd understandly be thinking "Zelda is so big, why isn't its main villain included?"
Obviously, Nintendo would want to include the revenue and popularity from TV shows, merchandise and so forth as well. That would push Pokemon up because of the anime and movies, for example. Analysts suggest the Mario franchise is worth $10 billion!
But the EarthBound and retro series clearly show that's not the only thing that matters. And I think Nintendo/Sakurai understand it shouldn't be the Mario and Pokemon show, so those two mega-series are going to end up "underrepresented" no matter what.
Sales are taken from vgchartz.com, Wikipedia or what I can find on Google if I can't find them in those places. Virtual Console sales are not included as Nintendo doesn't release them.
These figures represent sales as of now, which is what Nintendo would be considering.
Representation by video game sales, Brawl:
KEY: Sales/# of characters - franchise (# reps, total sales)
Average Brawl:
61.3 million - average sales of the 17 Nintendo franchises/universes included in the game
31.6 million - 33 1st party select screen slots totaling 1.04 billion in video game sales
28.2 million - looking at it as 37 move sets instead
Median Brawl:
17.8 million - Legend of Zelda has the median Nintendo character slot
17.6 million - Metroid is the median Nintendo franchise (9th best selling)
14.2 million - Legend of Zelda is also the median move set
126.6 million - Mario including spin-offs [1] (4 reps, 506.3 million sales)
84.4 million - Mario universe, including Wario and Yoshi (6 reps)
68.9 million - Super Mario main series only (4 reps, 275.7 million sales)
54.8 million - Pokemon, PT is one character (4 reps, 219.3 million sales)
43.4 million - Game & Watch handhelds (1 rep)
43.2 million - Wii Fit (0 reps)
36.6 million - Pokemon, PT is three characters (6 reps)
34.6 million - Donkey Kong [2] (2 reps, 69.3 million sales)
23.4 million - Animal Crossing (0 reps)
22.6 million - Wario [3] (1 rep)
19.1 million - Yoshi [3] (1 rep)
17.8 million - Legend of Zelda, Zelda is one character (4 reps, 71.0 million sales)
17.6 million - Metroid, Samus is one character (1 rep, 17.6 million sales)
14.2 million - Legend of Zelda, Zelda/Sheik are two characters (5 reps)
11.2 million - Kirby (3 reps, 33.5 million sales)
8.8 million - Metroid, Samus and ZSS are two characters (2 reps)
5.8 million - F-Zero (1 rep)
4.1 million - Game & Watch collections (1 rep)
4.0 million - Fire Emblem [4] (2 reps, ~8 million sales)
3.8 million - Star Fox (3 reps, 11.5 million sales)
3.8 million - Pikmin (1 rep)
2.8 million - Kid Icarus [5] (1 rep)
1.8 million - Ice Climber (1 rep)
1.3 million - R.O.B., Gyromite sales only (1 rep)
1.0 million - EarthBound/Mother (2 reps, ~2 million sales)
[1] Mario Kart, Mario Party, Paper Mario, Mario RPGs, Mario & Sonic, etc.
[2] Includes Diddy Kong Racing
[3] Wario/Yoshi in the title
[4] Can't find figures for the first two Fire Emblem games, so I guessed they sold around as well as the SNES games (0.6 million each?). This carries over into their numbers below since those were NES games.
[5] Can't find figures for Kid Icarus: Of Myths and Monsters
Compare Melee representation at the time when Brawl was being developed:
Average Melee:
57.3 million - average sales of the 13 Nintendo franchises/universes included in the game
29.8 million - 25 character slots for 745.5 million in video game sales
28.7 million - 26 move sets
Median Melee:
19.1 million - Yoshi has the median character slot and the median included franchise
16.6 million - the median move set is between Yoshi and The Legend of Zelda
66.9 million - Mario including spin-offs (5 reps, 334.6 million sales)
62.3 million - Mario universe, including spin-offs, Yoshi and Wario (6 reps, 373.9 million sales)
59.1 million - Donkey Kong (1 rep)
53.0 million - Super Mario main series only (4 reps, 211.8 million sales)
43.4 million - Game & Watch handhelds (1 rep)
41.4 million - Pokemon (4 reps, 165.6 million sales)
25.5 million - Kirby (1 rep)
20.2 million - Wario (0 reps)
19.1 million - Yoshi (1 rep)
15.0 million - Animal Crossing (0 reps)
14.0 million - Legend of Zelda, Zelda is one character (4 reps, 56.1 million sales)
14.0 million - Metroid (1 rep)
11.5 million - Dr. Mario (1 rep)
11.2 million - Legend of Zelda, Zelda/Sheik are two characters (5 reps)
5.8 million - F-Zero (1 rep)
5.3 million - Star Fox (2 reps, 10.5 million sales)
4.1 million - Game & Watch collections (1 rep)
2.8 million - Fire Emblem (2 reps, 5.5 million sales)
2.7 million - Pikmin (0 reps)
1.8 million - Kid Icarus (0 reps)
1.8 million - Ice Climber (1 rep)
1.6 million - EarthBound/Mother (1 reps)
1.3 million - R.O.B., Gyromite sales only (0 reps)
0 - Wii Fit didn't exist yet
Compare Smash 64 representation during Melee's development:
Average Smash 64:
52.0 million - average sales of the 10 Nintendo franchises/universes included
43.3 million - 12 characters for 520 million in video game sales
Median Smash 64:
25.0 million - median Smash 64 lies between Legend of Zelda and Kirby
14.5 million - median Smash 64 franchise lies between Kirby and Yoshi
103.6 million - Mario including spin-offs (2 reps, 207.3 million sales)
77.2 million - Super Mario main series only (2 reps, 154.4 million sales)
76.2 million - Mario universe, including spin-offs, Yoshi and Wario (3 reps, 228.5 million sales)
69.4 million - Pokemon (2 reps, 138.8 million sales)
46.9 million - Donkey Kong (1 rep)
43.4 million - Game & Watch handhelds (0 reps)
32.5 million - Legend of Zelda (1 rep)
17.4 million - Kirby (1 rep)
11.5 million - Yoshi (1 rep)
10.2 million - Dr. Mario (0 reps)
9.7 million - Wario (0 reps)
7.0 million - Star Fox (1 rep)
5.9 million - Metroid (1 rep)
4.0 million - F-Zero (1 rep)
4.1 million - Game & Watch collections (0 reps)
2.7 million - Fire Emblem (0 reps)
1.8 million - Kid Icarus (0 reps)
1.8 million - Ice Climber (0 reps)
1.3 million - R.O.B., Gyromite sales only (0 reps)
1.2 million - EarthBound/Mother (1 reps)
0 - Animal Crossing had not been released yet
0 - Pikmin did not exist yet
0 - Wii Fit did not exist yet
So, considering what could be added, let's think about who's in now and what series aren't in yet.
Smash 4 addendum:
43.2 million - Wii Fit (1 rep)
23.4 million - Animal Crossing (1 rep)
Unrepresented franchise sales:
177.7 million - Mario Kart/Sports/Party combined*
149.6 million - Wii/Mii games (Wii Sports, Wii Play, etc.)
95.4 million - Mario Kart
70.0 million - Wii/Mii games excluding Wii Sports since it was bundled
47.3 million - Mario Sports
35.3 million - Brain Age
35.0 million - Mario Party
28.3 million - Duck Hunt (was part of a bundle though)
24.3 million - Smash Bros
21.7 million - Nintendogs
11.5 million - Dr. Mario
8.7 million - Paper Mario
7.1 million - Mario & Luigi
6.2 million - Excite racing games
5.9 million - Luigi's Mansion**
>4.2 million - Rhythm Heaven
>4.0 million - (Advance) Wars
3.6 million - Golden Sun
3.6 million - Wave Race
3.1 million - Punch-Out!!
3.1 million - Pilotwings
2.1 million - Nintendo Land
2.1 million - Starfy
2.1 million - Super Mario RPG
>2.0 million - 1080 Snowboarding
1.8 million - Fossil Fighters
>1.2 million - Custom Robo
1 million - Balloon Fight
0.8 million - Xenoblade Chronicles (note: limited supplies, not demand!)
0.9 million - Chibi-Robo
0.7 million - Elite Beat Agents/Ouendan
0.5 million - Sin & Punishment
0.5 million - The Last Story
??? - Pushmo, Dillon's Rolling Western (digital sales figures unavailable)
*Combined sales relevant for consideration of characters like Waluigi who only has appeared in such games, and Daisy who primarily appears in such games
**Luigi's Mansion did get a level, but there's no LM-specific character and Luigi has no moves specific to it. The level of sales makes me think Luigi needs to use his Poltergust for something.
Not that this matters, but...
3rd party addendum, sales on Nintendo consoles:
>37 million - Sonic, >100 million total all platforms
~18 million - Mega Man, ~26 million total all platforms
~2 million - Metal Gear, ~35 million total
One of these is not like the others... Snake is very lucky his creator really wanted him in, because there's not really much reason to think he should be. Contrast: Castlevania is also by Konami, and a large portion of that series' sales are on Nintendo platforms (around 7.6 of 12 million shown on vgchartz, but games are missing. Wikipedia says the series has 20 million sales).
You can also see why Mega Man is a great fit - Mega Man has lots of sales on NES, SNES and Nintendo handhelds.
While sales aren't everything, I'm sure that Sakurai and Nintendo consider them. Beyond the polls of Smash fans, sales are also an indicator of who is popular, recognized and so forth among fans, including the less hardcore. I'd guess that they're more important when a series still has major cast members left out (as with DKC or Metroid). Zelda has its most important characters included, other possibilities would mostly be characters that only appeared in one or two games or are quite minor, so I think the sales is less important at this point. But if Ganon wasn't in, we'd understandly be thinking "Zelda is so big, why isn't its main villain included?"
Obviously, Nintendo would want to include the revenue and popularity from TV shows, merchandise and so forth as well. That would push Pokemon up because of the anime and movies, for example. Analysts suggest the Mario franchise is worth $10 billion!
But the EarthBound and retro series clearly show that's not the only thing that matters. And I think Nintendo/Sakurai understand it shouldn't be the Mario and Pokemon show, so those two mega-series are going to end up "underrepresented" no matter what.
Sales are taken from vgchartz.com, Wikipedia or what I can find on Google if I can't find them in those places. Virtual Console sales are not included as Nintendo doesn't release them.
These figures represent sales as of now, which is what Nintendo would be considering.
Representation by video game sales, Brawl:
KEY: Sales/# of characters - franchise (# reps, total sales)
Average Brawl:
61.3 million - average sales of the 17 Nintendo franchises/universes included in the game
31.6 million - 33 1st party select screen slots totaling 1.04 billion in video game sales
28.2 million - looking at it as 37 move sets instead
Median Brawl:
17.8 million - Legend of Zelda has the median Nintendo character slot
17.6 million - Metroid is the median Nintendo franchise (9th best selling)
14.2 million - Legend of Zelda is also the median move set
126.6 million - Mario including spin-offs [1] (4 reps, 506.3 million sales)
84.4 million - Mario universe, including Wario and Yoshi (6 reps)
68.9 million - Super Mario main series only (4 reps, 275.7 million sales)
54.8 million - Pokemon, PT is one character (4 reps, 219.3 million sales)
43.4 million - Game & Watch handhelds (1 rep)
43.2 million - Wii Fit (0 reps)
36.6 million - Pokemon, PT is three characters (6 reps)
34.6 million - Donkey Kong [2] (2 reps, 69.3 million sales)
23.4 million - Animal Crossing (0 reps)
22.6 million - Wario [3] (1 rep)
19.1 million - Yoshi [3] (1 rep)
17.8 million - Legend of Zelda, Zelda is one character (4 reps, 71.0 million sales)
17.6 million - Metroid, Samus is one character (1 rep, 17.6 million sales)
14.2 million - Legend of Zelda, Zelda/Sheik are two characters (5 reps)
11.2 million - Kirby (3 reps, 33.5 million sales)
8.8 million - Metroid, Samus and ZSS are two characters (2 reps)
5.8 million - F-Zero (1 rep)
4.1 million - Game & Watch collections (1 rep)
4.0 million - Fire Emblem [4] (2 reps, ~8 million sales)
3.8 million - Star Fox (3 reps, 11.5 million sales)
3.8 million - Pikmin (1 rep)
2.8 million - Kid Icarus [5] (1 rep)
1.8 million - Ice Climber (1 rep)
1.3 million - R.O.B., Gyromite sales only (1 rep)
1.0 million - EarthBound/Mother (2 reps, ~2 million sales)
[1] Mario Kart, Mario Party, Paper Mario, Mario RPGs, Mario & Sonic, etc.
[2] Includes Diddy Kong Racing
[3] Wario/Yoshi in the title
[4] Can't find figures for the first two Fire Emblem games, so I guessed they sold around as well as the SNES games (0.6 million each?). This carries over into their numbers below since those were NES games.
[5] Can't find figures for Kid Icarus: Of Myths and Monsters
Compare Melee representation at the time when Brawl was being developed:
Average Melee:
57.3 million - average sales of the 13 Nintendo franchises/universes included in the game
29.8 million - 25 character slots for 745.5 million in video game sales
28.7 million - 26 move sets
Median Melee:
19.1 million - Yoshi has the median character slot and the median included franchise
16.6 million - the median move set is between Yoshi and The Legend of Zelda
66.9 million - Mario including spin-offs (5 reps, 334.6 million sales)
62.3 million - Mario universe, including spin-offs, Yoshi and Wario (6 reps, 373.9 million sales)
59.1 million - Donkey Kong (1 rep)
53.0 million - Super Mario main series only (4 reps, 211.8 million sales)
43.4 million - Game & Watch handhelds (1 rep)
41.4 million - Pokemon (4 reps, 165.6 million sales)
25.5 million - Kirby (1 rep)
20.2 million - Wario (0 reps)
19.1 million - Yoshi (1 rep)
15.0 million - Animal Crossing (0 reps)
14.0 million - Legend of Zelda, Zelda is one character (4 reps, 56.1 million sales)
14.0 million - Metroid (1 rep)
11.5 million - Dr. Mario (1 rep)
11.2 million - Legend of Zelda, Zelda/Sheik are two characters (5 reps)
5.8 million - F-Zero (1 rep)
5.3 million - Star Fox (2 reps, 10.5 million sales)
4.1 million - Game & Watch collections (1 rep)
2.8 million - Fire Emblem (2 reps, 5.5 million sales)
2.7 million - Pikmin (0 reps)
1.8 million - Kid Icarus (0 reps)
1.8 million - Ice Climber (1 rep)
1.6 million - EarthBound/Mother (1 reps)
1.3 million - R.O.B., Gyromite sales only (0 reps)
0 - Wii Fit didn't exist yet
Compare Smash 64 representation during Melee's development:
Average Smash 64:
52.0 million - average sales of the 10 Nintendo franchises/universes included
43.3 million - 12 characters for 520 million in video game sales
Median Smash 64:
25.0 million - median Smash 64 lies between Legend of Zelda and Kirby
14.5 million - median Smash 64 franchise lies between Kirby and Yoshi
103.6 million - Mario including spin-offs (2 reps, 207.3 million sales)
77.2 million - Super Mario main series only (2 reps, 154.4 million sales)
76.2 million - Mario universe, including spin-offs, Yoshi and Wario (3 reps, 228.5 million sales)
69.4 million - Pokemon (2 reps, 138.8 million sales)
46.9 million - Donkey Kong (1 rep)
43.4 million - Game & Watch handhelds (0 reps)
32.5 million - Legend of Zelda (1 rep)
17.4 million - Kirby (1 rep)
11.5 million - Yoshi (1 rep)
10.2 million - Dr. Mario (0 reps)
9.7 million - Wario (0 reps)
7.0 million - Star Fox (1 rep)
5.9 million - Metroid (1 rep)
4.0 million - F-Zero (1 rep)
4.1 million - Game & Watch collections (0 reps)
2.7 million - Fire Emblem (0 reps)
1.8 million - Kid Icarus (0 reps)
1.8 million - Ice Climber (0 reps)
1.3 million - R.O.B., Gyromite sales only (0 reps)
1.2 million - EarthBound/Mother (1 reps)
0 - Animal Crossing had not been released yet
0 - Pikmin did not exist yet
0 - Wii Fit did not exist yet
So, considering what could be added, let's think about who's in now and what series aren't in yet.
Smash 4 addendum:
43.2 million - Wii Fit (1 rep)
23.4 million - Animal Crossing (1 rep)
Unrepresented franchise sales:
177.7 million - Mario Kart/Sports/Party combined*
149.6 million - Wii/Mii games (Wii Sports, Wii Play, etc.)
95.4 million - Mario Kart
70.0 million - Wii/Mii games excluding Wii Sports since it was bundled
47.3 million - Mario Sports
35.3 million - Brain Age
35.0 million - Mario Party
28.3 million - Duck Hunt (was part of a bundle though)
24.3 million - Smash Bros

21.7 million - Nintendogs
11.5 million - Dr. Mario
8.7 million - Paper Mario
7.1 million - Mario & Luigi
6.2 million - Excite racing games
5.9 million - Luigi's Mansion**
>4.2 million - Rhythm Heaven
>4.0 million - (Advance) Wars
3.6 million - Golden Sun
3.6 million - Wave Race
3.1 million - Punch-Out!!
3.1 million - Pilotwings
2.1 million - Nintendo Land
2.1 million - Starfy
2.1 million - Super Mario RPG
>2.0 million - 1080 Snowboarding
1.8 million - Fossil Fighters
>1.2 million - Custom Robo
1 million - Balloon Fight
0.8 million - Xenoblade Chronicles (note: limited supplies, not demand!)
0.9 million - Chibi-Robo
0.7 million - Elite Beat Agents/Ouendan
0.5 million - Sin & Punishment
0.5 million - The Last Story
??? - Pushmo, Dillon's Rolling Western (digital sales figures unavailable)
*Combined sales relevant for consideration of characters like Waluigi who only has appeared in such games, and Daisy who primarily appears in such games
**Luigi's Mansion did get a level, but there's no LM-specific character and Luigi has no moves specific to it. The level of sales makes me think Luigi needs to use his Poltergust for something.
Not that this matters, but...
3rd party addendum, sales on Nintendo consoles:
>37 million - Sonic, >100 million total all platforms
~18 million - Mega Man, ~26 million total all platforms
~2 million - Metal Gear, ~35 million total
One of these is not like the others... Snake is very lucky his creator really wanted him in, because there's not really much reason to think he should be. Contrast: Castlevania is also by Konami, and a large portion of that series' sales are on Nintendo platforms (around 7.6 of 12 million shown on vgchartz, but games are missing. Wikipedia says the series has 20 million sales).
You can also see why Mega Man is a great fit - Mega Man has lots of sales on NES, SNES and Nintendo handhelds.