I've played both versions (gave my original copy to a mate when I pickedup the GOTY edition used) and can't say I've noticed a performance difference in them - though the framerate is notoriously flaky on this game anyway...
Well Fallout 3 has always had a problem with the PS3 version. Mostly with freezes and glitches which can get quite annoying.
But most of those have been fixed now, so you shouldn't worry about it too much. I'm currently playing through the game again, and i haven't encountered any problems with it thus far.
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