Marvel Vs Capcom 3
The ability to triple select a character should have been in, but it couldn't be, of course, because the characters only have 4 colors, and you'd need at least six in case both players wanted a team of one character.
3D Marios
I've only played 64 and Galaxy 1/2, but I know in those you can't take items from one place to another. In fact, they have timers on them a lot of times. That's . . . not as fun. Being able to use an item and store another like in Super would be fun, even if game breaking. Just adding it as a bonus for completing all 242 stars would have been awesome.