To be honest I'm not very tech-savy when it comes to emulation and I have zero patience so if I can't fix it in a few minutes I generally give up, lol. I'm not really sure what GPU even is, lol. I assume it's graphics related?
The only game I've ever managed to get working at near 100% speed is .hack Infection. Pretty much every other game has differing severities of lag but fighting games seem to be the worst offenders (the old Naruto Ultimate Ninja games are unplayably laggy too).
I just assumed PS2 emulation isn't in a reliable state yet but since SCVI was announced I thought I'd give it one more shot.