What's new this time around? 3D, in two varieties. First, the game has been remade from the ground up with new polygonal environments and character models. Second, as a 3DS game, it features stereoscopic effects. The new art is ... hit and miss. In some areas, thanks to a rather dark "ambient" light and unfortunate camera angles, it can be difficult to see where a door is or to determine the location of a platform. But in some areas (like the Plantation and the Egg Corridor), the remake gives you a fascinating new look at a familiar area. The weirdly abstract background art in the Plantation is some of the most effective artwork I've seen in a game this year. I went in skeptical of the artwork and came out impressed. There's no denying, however, that the original Cave Story has the more memorable look.
Other, more gameplay-minded additions include a couple new areas, which are a lot more 2.5D in layout and camera movement than the old areas, and new difficulty settings. I don't mind saying I played on easy, which, as far as I can tell, just meant I got more HP upgrades.
How's it hold up? Before this most recent playthrough, I would have said "It holds up great." Following my experience in Cave Story 3D, I could see fit to append an exclamation point to that statement. Cave Story just seems to get better with age. It's surprising to see how, after roughly seven years, it remains at the forefront of the Metroidvania "genre." Rather than simply allowing you to play out of sequence, Cave Story actually features branching paths, with fully optional weapons, areas, and bosses -- hours of content that you can skip entirely, and you likely will unless you're specifically trying to get to it.
The mechanics feel identical to the original version, which is to say that it is incredibly satisfying just to move Quote around the screen. If you've played Cave Story before, you know how fun it is to use the machine gun to shoot downward and extend a jump. If you're new to it, imagine a gun that also works as a jetpack. Oh, and you also get a jetpack later.
Basically, all I can do is encourage you to play Cave Story, regardless of whether you get this version or the DSiWare version (or play it on PC, Mac, WiiWare, etc.) This new remake is, paradoxically, a good choice for neophytes interested in a well-designed shooter/platformer (because of the New Super Mario Bros.-ised graphics), or people who have played Cave Story a billion times (because of the new content and the fresh experience).
I love Cave Story. And I still love it in 3D.