Up through Chapter 3-2(?), some comments (I pretty much disagree with defensor, but I'd already played the GC one):
-Graphics are noticably worse. Not horrible, but anybody who tells you you're nitpicking is full of shit. 2 people over here (one's a non-gamer) who have never played either game but have watched me play both games commented on the graphics looking duller and more washed out as well as fuzzy, without any prodding from me. The fuzziness confuses me, since I playing on a component setup here, whereas I only have S-Video for my GC. However once you get out of the village, the colors do look MUCH better, just all the browns look poor on the PS2 I guess. Any graphical complaints in the Castle would be mostly nitpicking, but it's a definite issue in the village. I'm noticing a couple little things and here that are missing out of the GC version, mostly trees, but nothing that's a big deal. Also there's that weird afterimage/blur on the characters in the walkie/codec screen, not sure if that's intentional or not. If I wasn't skipping those anyway it'd probably bug me.
-Haven't noticed any of the slowdown there supposedly is. Had it once for a split second, and that was it, so far a non-issue.
-How the hell did they fuck up the sound?
-Load times don't really bother, although the load screen is realllllly lame.
-Controls are fine, after some playtime with the PS2 version I don't notice a whole lot of a difference either way honestly. I'm going to do the firing range range right now, that'll be the test for me

-Gameplay's all the same, although I swear that the game gives you a LOT more money than before (other people seem to be making that same comment), but you get less items. I've played through the GC version several times, but when I hit the 3rd chapter, I was actually out of healing items for the first time ever (even on my first playthrough) simply due to my lack of finding them, but I had an obscene amount of ammo (something like 500+ rounds for the handgun). Makes it a little different for a new playthrough, but I'm not sure if it's intentional, or I'm just lucky/unlucky.
-Story scenes are a mixed bag for some reason. Some look great, can't tell they're FMV, but then others look horrible, super grainy and obviously FMV, not sure what's up with that.
Right now my score for GC is a 9.8, I'd give the PS2 one a 9.0, mainly for the (noticable) graphical downgrade. Don't get me wrong, it still looks great and I'm still having a blast, but it's not as good. Seperate Ways may or may not make it all worthwhile

. If you have only one of the systems you're fine with whichever one you get, if you have both you're an idiot for waiting, I'd still reccommend buying the GC version, and renting the PS2 version for Seperate Ways, except for the few of us who are willing to spend the money and buy both ^^.