I believe that Sakurai doesn't want any one single franchise to dominate the roster. I'm pretty sure thinking otherwise is delusional.
Of course not, but whether it's 4, 5, 6 or even 8 character for a specific franchise doesn't matter in a game that has (likely) over 40 characters. That's only a fraction of that roster.
You have to understand that when the development team first decides on a roster, there's an estimation of how many characters they can make with the time and resources they have available. They get the obvious choices (for Smash, that would Mario, Link, etc.) out of the way first and then do the characters that they deem to be interesting inclusions in terms of gameplay.
If they estimate 40 characters, but can make only 36, then the game ships with 36. If they estimate 40 characters and have time to make 42, then the game might ship with 42 (unless they decide to spend the time/resources elsewhere, which also might happen).
Do you honestly think that Mr. Game & Watch made it into the Smash franchise because Sakurai decided that the "retro franchises" needed "2 slots"? Or rather because he felt that Mr. Game & Watch would make an interesting and fun inclusion as a character in terms of gameplay?
Especially considering that your "5 reps"-theory is busted by the very own link you provided with the left over files that were found on the Brawl disc. Brawl was originally planned to have 7 (!) Zelda characters - the 5 we got in Brawl AND Toon Zelda + Toon Sheik. Heck, Pokemon even has
6 characters already in the game, and Mewtwo was also planned, which would've made it 7, and the "pra_mai" files likely would've been Plusle & Minun, bringing it up to a total of 8.
Obviously, some of those characters have been scrapped somewhere down the line, and we don't know why, but it certainly would debunk your "omg we cannot have more than 5 characters per franchise" theory.