Let's try this.
STAGES.
WiiU version:
1. Battlefield (Smash Bros.)
2. Final Destination (Smash Bros.)
3. Mario Galaxy (Galaxy 1 & 2)
4. Bowser's Castle (composite of New Super Mario Bros., Mario 3D World and Mario Kart)
5. Oolong (Paper Mario: The Thousand Year Door) [chose this because many characters from other parts of the game could appear here)
6. Donkey Kong Island (Tropical Freeze) [normal beach area which gets freeze after a bit by the vikings)
7. Gangplank Galleon (Diddy's Kong Quest)
8. The Roof (Luigi's Mansion)
9. Diamond City (Game & Wario)
10. 1-1: Make Eggs, Throw Eggs (World 2: Yoshi's Island) [first moving Yoshi's Island stage]
11. Skyloft (Skyward Sword)
12. Desert Palace (A Link To The Past)
13. Dragon Roost Island (Wind Waker HD)
14. Pokémon Stadium 3 (Pokémon, dragon, dark, psychic, fairy)
15. Poké Floats 2 (Pokémon)
16. Pyrosphere (Other M)
17. Elysia (Prime 3: Corruption)
18. Palutena's Temple (generic Kid Icarus stage)
19. Sauria (Adventures / Assault)
20. Flower Fields (Kirby's Epic Yarn)
21. Bionis' Leg (Xenoblade Chronicles)
22. Smashville 2 (City Folk)
23. Wii Fit Training Room (Wii Fit)
24. Garden Of Hope (Pikmin 3)
25. Boxing Ring (Punch-Out!)
26. Wuhu Island (Pilotwings series)
27. From Pain, Awakening (Fire Emblem: Radiant Dawn ending map)
28. NintendoLand (NintendoLand)
29. Gyromite (R.O.B. stage)
30. Aeropolis (F-Zero GX)
31. Threed (Mother 2)
32. Windy Hill Zone (Sonic Lost World)
33. Dr. Wily's Castle (Mega Man 2)
34. Shadow Moses Island 2 (Metal Gear Solid: The Twin Snakes)
35. Stage 1 (Pac-Man)
36. Delfinia (Mario Sunshine, Brawl remake)
37. Rainbow Cruise (Super Mario 64, Melee remake)
38. Rumble Falls (Jungle Beat, Brawl remake)
39. Great Bay (Majora's Mask, Melee remake)
40. Bridge Of Eldin (Twilight Princess, Brawl remake)
41. Frigate Orpheon (Metroid Prime, Brawl remake)
42. Skyworld (Kid Icarus, Brawl remake)
43. Saffron City (Pokémon Red & Blue, N64 remake)
44. Lylat Cruise (Lylat Wars, Brawl remake)
45. Big Blue (F-Zero GX, Melee remake)
46. Fountain Of Dreams (Kirby's Adventure, Melee remake)
47. Halberd (various Kirby games, Brawl remake)
48. Fourside (Mother 2, Melee remake)
49. Summit (Ice Climber, Brawl remake)
50. Green Hill Zone (various Sonic games, Brawl remake)
3DS version:
1. Battlefield (Smash Bros.)
2. Final Destination (Smash Bros.)
3. Super Mario 3D Land (Mario 3D Land)
4. Rainbow Road (Mario Kart 7)
5. Chocolate Island (Super Mario World)
6. Sunset Shore (Country Returns 3D)
7. Yoshi's New Island (Yoshi's New Island)
8. Wario-Ware 2 (basically a remake of 1 with new games)
9. Secret Mine (Dark Moon)
10. Gerudo Valley (Ocarina Of Time 3D)
11. Spirit Tracks (Spirit Train)
12. Lumiose City (Pokémon X & Y)
13. Cerulean Cave (Pokémon Red & Blue)
14. Pokémon Center (various Pokémon games)
15. Meridia (Super Metroid)
16. Sector Y (Star Fox 64 3D)
17. Fichina (Star Fox Command)
18. Arena Ferox (Fire Emblem Awakening)
19. Reset Bomb Forest (Kid Icarus: Uprising)
20. Pandora's Labyrinth Of Deceit (Kid Icarus: Uprising)
21. Boxing Ring (Punch-Out!)
22. Tortimer Island (New Life)
23. Flat Zone 3 (composite of various Game & Watch)
24. Lollipop Land (Kirby: Triple Deluxe)
25. Lor Starcutter (Kirby's Return To Dreamland)
26. Distant Planet 2 (Pikmin)
27. Fire Field (F-Zero X)
28. Tomodachi Collection (Tomodachi Collection)
29. Nintendogs (Nintendogs)
30. Find Mii (Find Mii)
31. Mountain 1 (Ice Climber)
32. Casino Night Zone (various Sonic games)
33. The End (Metal Gear Solid 3: Snake Eater, forest area where you fight The End)
34. Stage 2 (Pac-Man)
35. Sigma Fortress (Mega Man X)
36. Mushroom Kingdom (Super Mario Bros., Melee remake)
37. Kongo Jungle (Donkey Kong Country, Melee remake)
38. Yoshi's Island (Yoshi's Story, N64 remake)
39. Pirate Ship (Wind Waker, Brawl remake)
40. Hyrule Castle (various Zelda games, N64 remake)
41. Brinstar (Super Metroid, Melee remake)
42. Pokémon Stadium 2 (various Pokémon games, Brawl remake)
43. Corneria (various Star Fox games, Melee remake)
44. Mute City (F-Zero GX, Melee remake)
45. Onett (Mother 2, Melee remake)
46. New Pork City (Mother 3, Brawl remake)
47. Dream Land (Kirby's Return to Dreamland, N64 remake)
48. Pictochat (Pictochat, Brawl remake)
49. Castle Siege (generic Fire Emblem stage, Brawl remake)
50. Shadow Moses Island (Metal Gear Solid: The Twin Snakes, Brawl remake)
Took me a while. I think it's pretty balanced. The only rule was 50 stages per version, 15 of which are remake. So, 70 new stages and 30 remakes (34 if you count Battlefield and Final Destination). I kept shared stages to a low (just the aforementioned two and Boxing Ring as announced as far), but many of them can share the layout. For example, Bowser's Castle and Rainbow Road, being both in part based on Mario Kart, can essentially be the same stage with different backgrounds. Technically, I think it would be easy to even take two stages from two different franchises like Garden Of Hope and Yoshi's New Island and use the same layout changing the visuals.
Some franchises appear only on the home console version (Xenoblade Chronicles, Wii Fit, NintendoLand, Pilotwings), some only in the handled (Tomodachi Collection, Find Mii, Nintendogs, Ice Climber), as far as new stages go.
I tried obviously to keep portable games' stages on the 3DS and home console's games' stages on 3DS, for example in the Zelda series, but not so strictly.
I think I got a couple of interesting choices there, and I would be incredibly fine with this list. Hoping at least we reach 80ish stages in the end between both versions.
I based the stage selection on this roster I made previously: