The only game genre I think that was really improved with 3D is racing games. I find I have more fun with a true 3D racing game than a fake 3D one most of the time, although 3D racing games aren't only modern. Stunt Car Racer is still the most fun racing game I have ever played, it's fully 3D but it's as retro as you can get. All they'd need is to remake the game with the exact same playability but with nicer, modern graphics and I think it'd be an instant hit (add online multiplayer too perhaps).
Apart from that though, I'm much more a fan of retro games. I really love looking at cell-based animation and pixel art, especially when it's been designed for the palette being used, and not just colour-reduced and remapped like most Amiga adventure games (although when they touched them up by hand like in Kings Quest VI it shows they cared more and the results are better). I don't like 2D games that are made up of vectors and simple hand-drawn characters that are scanned in and moved around the screen and rotated in real time. These things look like South Park characters or puppets or something.
Unfortunately the main reason we see less good 2D pixelled artwork in games these days is because it's a lot more time-consuming than regular game art (especially when a limited palette is involved) and it's more expensive to pay the artists, who generally have more experience in the industry and have been around since the days when pixel art was used more. There are still a lot of good pixel artists around, and plenty of younger people are still interested in the art form, so provided someone can get a full game finished and not give up half way through, we might see some new games in the future using that classic, intricate pixel art once again.
