This isn't a hardware issue, it's just that flash really really sucks on OS X. For some reason Adobe has taken it upon themselves not to bother optimising flash for macs, if you have iStat Pro installed check the CPU readings during youtube playback and you'll see it can take up to 100% of the CPU.
I was actually looking this up the other day because youtube was getting choppy and using about 70% of my CPU, turns out this is a common problem. What I would say is make sure your flash player is up-to-date. I downloaded 10 and my CPU usage went down to 50% and the videos weren't choppy anymore, I guess I must have been on 9 without realising.
Still, 50% CPU useage for a youtube video is pretty unacceptable in 2009, come on Adobe, pull your finger out!