Well i will say, the 3DS version HAS at least improved considerably since the E3 2011 build. Still not an ideal version, but i'd have to say that looking closely, the raw visuals are at least as good if not a little better than the PS2 version, relatively speaking for the most part. Some instances even have higher res textures than the PS2 version, though some details like the finger textures are lower quality. Polygon counts seem very solid, about on par with MGS3 on PS2. Though i did notice a lower polygon count. It's on Snake's shoulder right after he dives into the jungle and unmasks. You can notice his shoulder is blockier than the original. And in some cases, it seems that the background jungle foliage may have been toned down slightly.
Lighting and shader effects have improved somewhat. Some textures now appear to have normal mapping applied. You can see this on Snake's jumpsuit in the plane and during skydiving. Glad to see they're making SOME use of the 3DS' more advanced visual hardware. Konami also re-instated the reflection effects on Snake's goggles when the plane hatch opens (was missing in the E3 footage). This goes for depth of field as well (some of it anyways). So there's a bit of a balance of downgrade and upgrades.
Unfortunately the thing that really killed the 3DS version from the beginning is something that was never fully fixed. The framerate (at least in cutscenes) is still as choppy as ever (and you can't see this in shots, go watch a video of it). We're talking framerates dipping into the teens and sometimes even single digits. Considering the time they've had to develop the game, and the hardware power advantage 3DS has over PS2 (mentioned by Kojima himself and proven with the Naked Sample demo), it's a damn shame they couldn't at least stabilize the framerate before release. I'm not entirely going to take IGN's word until i've seen actual ingame footage. Had it not been for this, the 3DS version would at least have been a good version of the game technically speaking. If i'm wrong and the game actually plays better on the actual system, i retract my statements.
Overall, i find this game very lazy. Looks unfinished, like they needed at least another 4-5 months to optimize it (which is ridiculous considering how much time they had). Not the worst "remake" i've ever seen (that might go to Sonic the Hedgehog on GBA), but still kind of shitty. Visual improvements are nice, but a better framerate would have been ideal. It's a bit of a dick move after witnessing the Naked Sample and what COULD have been.
I've screengrabbed some comparison shots from Youtube. PS2 vs 3DS. Just know that the PS2 shots have a quality advantage, the footage appears to have come from the game running on an emulator and is higher resolution than the actual game (only other option was to use low quality footage, which i didn't deem fair). Also excuse the compression artifacts, the 3DS version will look somewhat less blurred on a real 3DS due to being played natively in its own resolution. But anyways, here's the comparisons, PS2 on the left, 3DS on the right. Spoiler tagged because of the large quantity and size)-
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