Contra could be bad-ass! Just not as an FPS please. Crystalis is amazing! A 3D version could also be amazing! Or just put it out on the VC. Either way is fine. Half of me would love to see a 3D remake of Faxanadu. Half of me not so much. Breath of Fire Splatterhouse Zombies Ate My Neighbors could be so much fun. Ooh how about Metal Storm? X3 I love that game. I'd like to see a 3D iteration of Q-BERT and Kickle Cubicle. Revamped StarTropics would be interesting.
The only game that I can think of that might be good in 3D is Vectorman. I read that it was coming to PS2, Xbox and Gamecube and was gonna be a third person shooter but it looked and played to much like Halo (I don't hate halo. It's my 3rd favorite shooter series. Behind DOOM series and Turok series), regenerating health, using guns instead of energy bolts fired from he's hand and the appearance of Vectorman was crappy. Fortunately the game was canned due to so much negative response from fans. Kinda like what happened to Metroid Prime: Federation Force only MPFF wasn't cancelled Most of the classic 2D games have gone to 3D. Some have gone to great success. Others, not so much.
3D Final Fight exists and it was most definitely not cool. As far as Sega goes, you've got Dynamite Deka and Spike Out in that genre even if they didn't to Streets of Rage. Plus Yakuza, which is pretty much a beat 'em up structured as a Japanese open world game.
Jazz Jackrabbit needs a good 3D entry. I'd say Turrican does too, but that would really just end up being a Quake II variant with cool chiptune music.
I sometimes think I'd like to see the first two Zeldas +Link's Awakening DX in 3D. At other times no.
