I agree that Final Smashes were extremely unbalanced, however, I would like them to stay as optional. Its fun to use once in a while if you're not playing competitevly, and the various attacks (like the Smash of Game & Watch) are awesome to watch, and often make for really humorous situation IMO.
So, since everybody else is posting their dream additions, I might as well do it. There is an emphasis on dreaming here though:
Firts Party:
Little Mac - just let him play as a normal boxer, no reason not to include him if Nintendo is serious about keeping Punch Out! in the spotlight. I guess Punch Out Wii! sold enough for that.
King Hippo - he should be included for his awesome looks which is iconic. Could play as a slower version of Little Mac
Isaac - as a lot of people have mentioned, having a guy from Golden Sun would be smart. Make him a combination of a sword-guy like Marth and Pokemon Trainer with the Djinns, and he would be unique enough. Also, I would hope his inclusion woud help Camelot becoming an rpg-developer fulltime again. I have no interest in the sports games they keep making.
Ridley - this one is most obvious of all. Even though he probably should be a heavy character, I would make him light and give him awesome flying capabilities for balancing.
King K. Rool - again, he should be included for his awesomeness.
Cranky Cong - There is probably no need for him, but he is just so awesome that he need to be fitted in there somehow. The wheelchair makes him stand out a bit at least. (Funky would also be sweet)
Samurai Goroth - I always played with Goroth in the original, and thinks that he is the F-Zero character outside of Falcom with the most personality. Also, I would LOVE to see Nintendo use their F-Zero franchise to make a heavily driving based open world game set in a grim F-Zero-future. Is so, it would make sense to highlight a few other characters from the franchise.
Kamek/Magikoopa - we need an extra koopa, but the normal ones are a bit to boring. Kamek on the other hand, would be awesome.
Demon Lord Ghirahim - Would make sense after his inclusion in Skyward Sword.
Zant - another villain from Zelda. I loved to battle him in TP, so would be nice to use that battle as a template for how he would fight.
Mike - from Star Tropics. The jojo is good enough reason.
Realistically, I don't think there will be a ton of third party-characters, and it makes sense to keep the rooster to characters who most people associate with Nintendo-systems (which is why Solid Snake, for all his awesomeness, is really a bit strange). Anyways, here are a ton I would love to see included even though they are not all primarily associated with Nintendo:
Mega Man - this is the most obvious I guess. He is almost synonymous with the NES, making his best reason appearances harken back to that era. Let him be portrayed like an 8-bit character like Mr. Game and Watch.
Simon Belmont - goes without saying as well I guess
Pac-Man - for his legacy. Have no idea how he would play.
Knuckles - I loved to play as Knuckles in Sonic 3 & Knuckles thanks to his awesome gliding abilities. Should keep that somehow.
Dr. Robotnek - here there is potenial for all kinds of awesomeness with his machinery. Makes to much sense.
Slime - Dragon Quest is more or less Nintendo-property now, so it would be fun to have this iconic character appear. Have no idea how he would play though.
Leon Kennedy - would probably play similar to Solid Snake.
Raiden/Ocelot/Liquid - it would be nice to have another character from MGS, but I guess Konami should commit to release the series on the Wii U for that to be of any interest of anybody.
4 Warriors of Light - it would be fun if they could come up with a way to let all four play as once, as they did with the Ice Climbers. If not, then changing classes on the fly could also be cool.
Monster Hunter - huge-ass sword and slow movement, could make a pretty tactical character.
Travis Touchdown - Should also be included for his awesomeness, and to help sales of No More Heroes 3 on the Wii U
Ryu Hayabusa - this one I feel is actually the most realistic of them all with how close Team Ninja and Nintendo are lately.
I would also love to see Danté from DMC, but as he have never been on a Nintendo-system, I guess that's a bit far-fetched.