The Neo Geo is an incredible gaming experience. I've had several throughout the years (arcade MVS machines as well). They sure maximized the processing power in that puppy. There's even a 68000 in it IIRC. Both Baseball Stars, League Bowling, Last Resort, Metal Slug, King of Monsters, Umm... I'll just stop there. There's waaay too many great games for it, although you can have all those generic fighters they kept pumping out in the mid 90's. Yuck.
Dual 12MHz 68000, IIRC. And I envy your experience of owning NeoGeo MVS. I absolutely loved "Last Resort" and would play the hell out of that game at the local diner. Best part about the MVS was the headphone jack. I could immerse myself in the game and not bother patrons. It was like stepping out of another world when I finally finished.
As for 3D, I think the best and most exciting 3D games I ever played were "Looney Tunes Racing" on the Dreamcast, "CyberSled" (arcade and Playstation,) and "Crimson Skies" on the X-Box. I really enjoy realistic, first-person games -- not so much shooters. I played one of the Star Wars release in which you get to fly a TIE Fighter... that was pretty neat, too.
But I have a good bit of disdain for some of the 3D games out there now which seem to be just 3D and no real meat. Someone else mentioned that the 3D does not add to a lot of games, and I have to agree. I want substance in 3D. Unfortunately, a lot of 3D games I have played are nothing more than textured 2D characters superimposed into a 3D space. Really sucky.
Unfortunately (or perhaps not) I cannot partake of "modern" consoles because the screen modes trigger headaches in very short order. Displays which output 120Hz and above delay the inevitable, and a friend has a unit with software interpolation which reduces the effects of motion which also seems to help, but eventually the piercing pain hits me, and in a bad way, too, accompanied by motion-sick-like queasiness.