I've been going back and playing a lot of Marvel Ultimate Alliance lately, and with the sequel on the way, I thought I'd put together a wishlist of things that I'd like to see improved in this version.
First and foremost, fix the glitches. MUA was glitchy as hell, and it would be completely retarded for a good portion of them to not be fixed this time around.
There are lots of fun characters that simply aren't as effective as the powerhouses. If you're going to have a character who's deal is more than just big numbers, PLEASE boost their effectiveness so that they're not completely worthless. A lot of the buffs could be a lot better, and maybe have specific character-targeted buffs (i.e. extra armor for Hulk) to balance out the fact that they're more useful.
Better Boss Fights
Most boss fights in MUA are either 1.) Minigame driven or 2.) a normal enemy you can't stun/control with a lot of health. It never feels like you're fighting a real supervillian. Give them a weakness, make them more powerful, and make them susceptible to SOME form of status effect. Too many powers become useless when fighting bosses.
Better, Independent Online Play
Online play in this and all previous iterations of the game were essentially the same as playing locally. Instead, characters should be allowed to go wherever they please, and have their camera follow them. This allows you to actually split up if you need to, and you're never trapped because of where your teammates are. I think this would do a lot to boost online play, and could really step the game up to the next level.
The ability to have Spider-Man's web bullets hold enemies in place on hit or to have Human Torch's fireballs explode OR do burning damage creates a lot of interesting options, and gives players the ability to further customize their characters. The implementation can be tricky, but the key is to have as many different options as possible, without giving any one of them a clear advantage over the others.
Better Equipment System
The equipment in these games can end up somewhere between Baldur's Gate: Dark Alliance, and the original MUA. X-Men Legends toyed with the idea, but I think there's a lot of room here to play with different options for characters - with equipment providing a wider range of bonuses. Some of the items in MUA are really interesting, while others are a boring "+10 Striking." I think you can really mess with this, toy with different kinds of damage boosting, and make all the stats clearly visible.
This is straightforward, add some branching paths, make the environments more interactive and destructible, and make doing these things matter.
Give the enemies a larger variety of attacks. Give them more interesting, varied bonuses. Instead of making them resistant to all powers, make them resistant to Electricity, or Ice damage. Give their attacks some interesting properties, and don't let any attack be guaranteed damage. Make the players have to think about more than "our damage numbers need to be higher than theirs."
That's it for now. It's too late to push to get any changes made to the game, as it's releasing in the next quarter, but here's a quick list of things I'd really like to see them do.