I don't know whether it's the rushing that is making the game look so shitty. It may be that Konami just sent it off to a cheaper amateurish division that doesn't know what they're doing. I'm inclined to think it might just be the latter though. I guess we don't know exactly when the game started development, but the Naked Sample demo was shown at E3 2010. So assuming development on the port began soon afterwards, that's well over a year and a half of time that they had to make it. Porting a game decently shouldn't take that long. I'm more inclined to say that the team handling it is just lazy or don't know what they're doing.
Regardless though, in the right hands and with proper development time, there's no reason the game couldn't look and run just as good as the PS2 original. Better in fact, they seem to be completely squandering the 3DS' advanced shader hardware (even seen in Naked Sample).
From the footage, even the lighting is worse. 3DS can do normal mapping, self shadowing, real time soft shadows, hdr lighting, etc. Normal mapping coupled with good lighting and shadows could even have supplemented lower polygon models if need be. The only scene i've seen using any sort of 3DS specific shader effects is the skydiving cutscene on Snake's jumpsuit (and that is literally the only part of the game that looks better than the PS2 version). At the very least, 3DS is a beast at lighting and normal mapping. There's no excuse for the PS2 to come out on top in the lighting department.
I don't mean to sound like a troll, but that's honestly how it stands. 3DS is superior to the PS2 spec wise, far superior. To make a bad joke- Capcom does what Konamisn't.
I'd be very glad indeed to be proven wrong and have the game become competent during the remaining months before release. I don't expect to be wrong though, game hasn't gotten any better since E3. Though i have seen dramatic last minute cleanups before. It would still be upstaged by the Vita port, but at the very least it could become a competent port of the PS2 version if they're even going to bother porting it to the 3DS...