Much of the fun of Mario 3 was the ability to use any powerup anywhere. The one thing I wish they would have changed in Mario Galaxy is that when you get a powerup, you know it's exactly supposed to be used in these special little circumstances. Sure, it was weird using the Frog suit on a land level, or the flying tail in water, or whatever, but it was fun!
As an extension of this, powerups are few and far between. I want some useless powerups! I want to have to figure out which one I need. I could see for instance, using Ghost Mario underwater, to float through a drain to find a secret level or something. Ok, the Bee outfit couldn't work underwater
And why can't we have a real fly suit? I could see that one having to be limited, because it would make some levels just way too easy. But kinda like how Yoshi couldn't go into Ghost houses in Mario World, they could take the fly suit off when it just needed to go.
Well, I'm only halfway through the game, but these are the "flaws" I see in the basic design so far.
Not that it isn't the best game I've played in 10 years (or whenever Mario 64 came out), because it is. I just miss the superb powerup abilities of Mario 3. Not necessarily the same powerups, but the same variety, plentifulness, and ability to use them when you want (and store them).