The game is a pretty strait port of the PS2 original. Though so far, it bears some amount of downgrade. The framerate is considerably lower and more inconsistent than the original, textures are of lower quality, and a couple of the models are built with slightly fewer polygons. An impression at Nintendo Everything was particularly scathing about the framerate (which according to them, drops excessively ALL the time) and the controls. I can't speak for the latter, but the framerate definitely took a dive. The only upside i've noted was in the E3 trailer, which showed some superior lighting and shader effects on Snake's skydiving jumpsuit.
It's sad to see that Konami apparently took the easy way out. There's still more than enough time to clean the game up thankfully, but it's still a far cry from the apparent remake they were teasing last year. Naked Sample was quite impressive and teased everyone. In addition to that, Kojima said if he made it into an actual game, it could look far better (he claims the Naked Sample was rushed, and he has echoed many developers by saying the 3DS is far more powerful than PS2). It's a bit unacceptable since the 3DS is around GC or Wii power, it can't even handle a PS2 port...
We need to wait to see how the final game holds out. I'm not too positive however. Looks like they decided to just quick port it and take the easy way out. We'll see though. It's still inevitably not going to look much better than the PS2 version, and stands to look worse so far. At least the small screen will benefit and it will be in 3D though.