I've been having the same vibration problem with GS300 brakes since I've owned my '94 (bought it in '00 with only 49K on it). It's most annoying. I don't even drive it hard, so there's no real reason to have ANY brake problems in a car like this. Am now preparing to replace the front rotors again, after probably 60,000 mi.
Anyway, I've owned four MR2s in the 14 years before getting this car, and I NEVER had warping problems in any of those fun cars. And I drove them hard, as they were an absolute blast to drive.
Am now going to try cross-drilled and slotted rotors, as I'm guessing that it's a cooling problem that is warping them. The only "hard" driving I do with them is coming down off-ramps at a relatively high rate, but I'm still babying the car otherwise. Have read elsewhere that sitting with brakes applied at a light after such braking can keep too much heat on that portion of the rotor while stopped; sounds good enough to me after all these hassles!