It is truth in this world that money talks. Therefore, I'm going to show the ratio of character for every million copies of games in that series sold (note: Wario is counted with Mario, but not DK). Technically, the lower the number million copies sold per character, the more "overrepresented" a series is.
Mario Series (193 million copies, 5 characters, with a sixth, Luigi, leaked): 1 character for every 32 million copies sold
Pokemon (155 million copies sold, 4 characters already confirmed, since I'm counting each of the PT's pokemon): 1 character for ever 38 million copies sold
Zelda (52 Million copies sold, 2 characters officially so far): 1 character for every 26 million copies. If Zelda can turn into sheik, making it 3 character, it's 1 character for every 17 million sold. If Gannon also makes it, it's 1 character for every 13 million sold.
Donkey Kong (48 million copies sold, 2 characters so far): 1 character for every 24 million copies.
Kirby (30 million copies sold, 3 characters so far): 1 character for every 10 million copies sold.
Metroid (13 million copies sold, 1 character so far, 2 characters if you count Zero-Suit, which I will): 1 character for every 6.5 million copies sold
Sadly, I couldn't find good sales stats for Star Fox, Mother, Kid Icarus, Ice Climbers and the other games. I didn't include the third parties, since they're stats would be skewed by the fact they have only been on Nintendo consoles for intermittent amounts of time.
So, by this ranking, POKEMON and MARIO are the two least represented franchises, and KIRBY and METROID are the two most over-represented franchises. I know these stats will get me flamed (puts up shield), but I just thought that, given the fact that the number one goal of a video game is to MAKE MONEY (all the innovation, fun value, playability and general entertainment is only to reach that goal), that this could be a good way to look at it.
I don't agree with these ratings, by the way, as they favor older franchises (Mario) and franchises that crossed into the mainstream for periods of time (Pokemon).