I would invest a million dollars into developing a way to avoid panty shots for Amy in a 3D game.
It's easier to just redesign her clothes or use camera angles that keeps them out of sight. Then again after watching the mod of Generations PC I don't think it's that much of a deal since her boots and constant movement would hide them. Also there is the other resource of using animations for comic relief where she struggles to keep her underwear from being seen. (for example in advance 2/3 where she pulls her dress down during rail grinding)
Her hammer should probably be the core thing about her. It adds a bit of humor and can be somewhat frightening. Having a hammer that's capable of cracking ground and doing all kinds of things in certain situations. Perhaps make it almost godlike, but based on her amount of rings or ring loss that can result in a sorta magical/powerful action -- or emotion. Like, if she's being overwhelmed by enemies and the player clicks a button, Amy sends out, in a desperate attempt, several hammers and knocks them away. Humorously, it can go dark and scary looking during the magic attack, but come right back to sunny beaches and sunshine everywhere. Which is common for Amy in some impressions -- she's quick to change emotion.
And of course, running fairly quickly, and using her hammer to help her out. I guess she'd be a get to the end type of character. Meh.
Have her play like in Sonic Advance, plus rolling.
^ Pretty much these two. I'll add a few things-for the Adventure gameplay, I would have Amy run around the same speed of Tails, but with faster accelerations. For her Advance gameplay, I would also have her be able to roll also with slightly faster acceleration.
She wouldn't be a main story playable character, more of a side character you could unlock. As for gameplay, it just depends on the type of game. I think her hammer works a lot better in 2D then it does in 3D for Sonic games.