Certainly, Xenosaga takes the cake for overuse of cutscenes in video games, and also overuse of needless FMV that was just pre-recorded real time graphics. I guess since he was working with a DVD9 Takahashi didn't give a shit about optimizing the XS engine.
I'll say that MGS2 didn't have too many cut-scenes...it had a SHIT LOAD of codec interruptions. Are you sure some of you aren't confusing the two?
Anyway, MGS2's cut-scenes aren't all that professional-looking, at times they look downright amateurish by film standards, with the excessive zoom-ins, slow motion and whatnot. They are not God's gift from heaven. The CG in most games have better direction and editing, I'd say. I guess that compared to other real time cutscenes they are the best, but that's not saying much really. Most real time cutscenes are complete SHIT.
Kojima is no film director, that's for sure.