I have 2 computers (3 actually, but 2 I installed ME recently). On one of them, the newer one, I don't have any problems. On the other I get stuttering. Not as bad as you report, but annoying enough.
The one with the problems:
Athlon 64 X2 4200+
2 Gb DDR2
Nvidia GeForce 9800GT
The one without problems:
Intel i5 2500k
4 Gb DDR3
AMD Radeon 6850
Disabling some options like V-Sync did make it slightly better. The weird thing is, when I looked for solutions, there were quite a few recommendations to downgrade the video drivers. You normally are asked to make sure you have the latest drivers... I didn't try that cause like I said, the stuttering wasn't that bad that I'd risk messing other games, and the drivers that people recommended were something like version 169 or older I think. I don't remember exactly the version but they were older than my video card model...
The thing is, something like that might work. For one thing I don't remember having any problems way back when I first played ME. And on my new computer I have an ATI card, while people who complained about stuttering and recommended downgrading all had Nvidia, just like my second computer. If it's as bad as you say, I'd try a downgrade. Or use an ATI card, even older, if it would be an option.