360 controller: D Pad I guess, even though I dont have trouble with it when it's used for weapon selection and stuff, I know it's supposedly bad for 2d fighters (though I'm not sure if that's true either, I do know I actually kinda prefer the stock 360 controller to my mad catz fight pad for SFIV)
Other than that I'm not sure the 360 controller can be improved much. It's damn near perfect. I think controller evolution may have reached the end of the line.
I used to want 6 face buttons on the stock 360 controller, for Streetfighter games, but I'm not sure it would be good for every other genre of games on the planet, where 4 is probably more intuitive, so I'm not sure about that now.
PS3: Make it like 360 controller.
Oh and of course I guess, maybe make 360 controller rechargeable? I'm not even sure though because for me, I've got that problem licked. What I do is buy a 48 pack of Best Buy Dynex Alkaline AA's (basically store brand). These run $15 but I think last time I got them on sale for $11 or something, so they're cheap. They are pretty good batteries and last a while, and with a stash of 48 you're basically good forever, (or at least a year or two+, theyre also handy around the house, christmas morning etc).
Then you dont have to even worry about the whole recharge thing.
The problem with the recharge thing for me is my couch sits outside cord range to my TV, even the 360 9 foot play n charge cords or whatever. With a play n charge kit, you're still corded, and it still wont reach my couch. Let alone the 1.5 foot PS3 charge cord. So then I have to move, which I dont want to.
Although I guess you could be sure to plan ahead and charge when you're not playing (like I do with PS3). It's just one more thing to think about.
So rather than mess with it I just use the AA's as above. I guess if they make it rechargable, do a 15 foot cord...I'd probably be cool with that. Just make it still able to take regular batteries, be able to replace the rechargeable pack, and not all sealed up like the PS3 controller battery, so if it starts wearing down it's no prob.