There's a lot of stuff that could be added. First, make Samus as good as she was in melee!
Secondly, I always thought that they should have more characters. Here I'll make a shortlist of who I think they should add;
-King Karool(sp?): They just added Diddy but they still need to add in the evil guy from DK. Most series included in Smash(Mario, Zelda, SF, etc) have their evil guys, but DK doesn't.
-Dixie Kong: I read somewhere they planned to put her in Brawl but they didn't. An extra DK character wouldn't hurt. She would have a very good recovery and I think she'd fit the Smash roster.
-Megaman: Not a Nintendo exclusive, but Snake isn't either. He could have a pretty interesting moveset, including a charge beam like Samus, that can alternativly be spammed uncharged(like in his games). He could also do wall-jumps on 1 wall, like in his SNES games again(at least the X serie). It would be nice also to be able to switch to other weapon types(those you receive from defeating bosses in his games again). That would make him a very versatile character, probly more then PT himself. I could also see his final smash being that move he had in Marvel vs Capcom(where he became big and shot missiles).
-Zero(taken from Kraryo's post, if Megaman is in): Another interesting add-on to the roster. He would have similar moves to Megaman, but with his Z-Saber, and enough differences to not be a clone.
-Tails: Seeing as they added Sonic, his little partner wouldn't be too much asked. He'd probly be very similar to Sonic, with a few differences, like the ability to fly.
-Krystal(taken from Kraryo's post): It would indeed be nice to have a new SF character that's not a semi-clone. They shouldn't remove Falco tho, he's probably the most popular SF character in Smash games. I also find him more iconic then Krystal is, but still. We need a new SF char, not a "semi" new one.
-Lloyd Irving and Kratos from Tales of Symphonia: Not clones, but these two could make interesting add-ons. It would just give us more swordsmen to play with. They shouldn't be too hard to make either. They could even have Sword Rain(mashing jab button), and also other moves they have in ToS that wouldn't be hard to make, like Demon Fang.
-Colette from ToS: Another character that would have an interesting moveset. Give her flying abilities, and some long-ranged moves with her rings.
Enough with characters let's move to other stuff. A multiplayer boss mode could be interesting. Not that mode in Brawl, but a mode where one character picks a boss and the other has to defeat him with a regular character. Sure, it makes unfair matches and all, but it would sure as hell be fun. And it's not like you'd get to use the bosses in ordinary match-ups. It's something my friends and I used to do in melee. Make a 3v1, put the loner with high handicap, and the other three with low. It sure as hell makes interesting match-ups, and somewhat replicates a boss fight. But yeah such a boss mode would be nice.
I could probably find more stuff, but I'm getting out of ideas for the moment.