Personally, 40 individual characters would be my ideal number.
Here's what I'd do:
Characters I'd Remove-
Wolf (The character doesn't even play a significant role in the SSE and I think that alone says that he was a character addition that had very little thought put into it.)
ROB (Self explanitory and, unless you're completely brainwashed, you know his significance to Nintendo's history is laughable at best.)
Jigglypuff (To this day, I still have absolutely no idea why that thing is still playable because it's significance to the Pokemon franchise is trivial at best.)
Changes I'd Make-
Declone Ganondorf and let him use his sword for at least some of his attacks.
Declone Toon Link. (I personally believe the developers shot themselves in the foot with this character simply because they squandered nearly all his potential. The Deku Leaf, Skull Hammer, and maybe Ice and Fire arrows would have been nice additions. Heck, they didn't even give him the grappling hook or his crazy sword spin attack. It's a real shame.)
Characters I'd add-
Geno (Unique in nearly every possible faucet from moveset potential to character design. A definate homerun)
Krystal (Self explanitory to even people who are comatose.)
Ridley (Another no brainer decision.)
Megaman (A third party character that has been mostly loyal to Nintendo since the NES days, has appeared on every Nintendo platform except the Virtual Boy, and has close to 80 games under his belt. I'm more then convinced that Snake and Sonic were added merely for hype and, historically, neither of them has really contributed that much to Nintendo. Snake has 2 Nintendo exclusives and Sonic didn't join the "Nintendo cause" until 2002. In his own regards, Sonic's understandable because of all the GBA and DS exclusives and the old rivalry between Nintendo and SEGA but Snake is so out of place that it's not even funny...)
Isaac (Golden Sun recieved awesome reviews but I still believe that it's one of the most underrated Nintendo games ever made. That and SMRPG to me are like Beyond Good and Evil and Psychonauts. Apart from that, Isaac also brings a lot of interesting moveset possibilities to the table. Ragnorok as a final smash, anyone?)
Takamaru (A wandering Samurai who fights not only with a katana but also various ninja skills like surikens. What's not to like? The fact that all he is in Brawl is a trophy is beyond criminal.)
Mewtwo (The fact that he was the only unique character that was removed from Smash Bros simply because the developers scewed up with him the first time around is a slap in the face to the fans. I've never really liked the character that much but I'd definately put him back in with a new moveset in order to please his fans.)
Sukapon (Another japanese character that many people don't know about but, unlike ROB, is truly sigificant to Nintendo. He was the star of Nintendo's first true fighting game: Joy Mech Fight. Because of his unique character design and fighting style, he also brings a lot of interesting moveset possibilities to the table and would definately make a nice addition as a WTF character.)
Well, that's about it. All the people I mentioned to correspond to what Sakurai and his staff showed interest in the journal: Geno (5 entries), Krystal (3 entries), Ridley (4 entries), Megaman (2 entries and the only truly third party character that was mentioned more then once), Isaac (2 entries), Takamaru (3 entries), and Sukapon (2 entries).*
*Of the probably 300 characters that were suggested in the Japanese poll, only 21 of them were mentioned more then once.