Re: Protoss vs. Alien Grey
I'm a fan of the old Star*Drive setting, which also takes place ~2500 and seems to have roughly the same tech level, too.
In that setting, the fraal (what they call greys) are physically weak, but virtually every fraal has the power of suggestion (limited mind control), and about 1 in 5 are mindwalkers (psychics). I doubt 1 in 5 protoss are members of the Templar Caste.
On the other hand, their max power level isn't nearly as high as that of the protoss. Psionic storm would probably give them heart attacks from sheer fear, and of course they have nothing like archons.
Unlike in most other settings, the fraal technology isn't that much more advanced than that of humans, so they'd fail in the starship fighting department. I don't think they have a solution to protoss shields either, although that might not come up when you're giving telepathic suggestions :)
Re: Protoss vs. Alien Grey
Protoss, because they have no orifices (that we know of!) to stick a probe into :p.