You could possibly setup the brakes to work with reasonable balance, but you will be far from getting the best performance from them.
It would take an adjustable bias adjuster, and a low coefficient eduro compound pad in the front, and a high coefficient compound in the rear of the car. Along with high quality fluid and ducting on the rear brakes, you'd get away with it.
But carmikey probably has the best thought process on this. What pads and brake fluid are you running? And what kind of fade? Boiling the fluid (pedal travel increases/ goes soft) or pad fade (pedal stays hard, but stopping distance increases)
Switch to a high quality fluid, with a high boiling point. Also once you have boiled brake fluid, you really need to rebleed or flush the fluid. High performance pads are also needed to allow for repeatable braking performance.
Also airflow to the brakes can improve perfomance as well. Whether it is a basic air guide bolted between the caliper mounting bolts or a proper ducted unit , keeping temps in check can go a long way to helping. I dont know if anyone actually makes them for mr2 calipers, but look for titanium anti rattle shims. They effectively act as a thermal barrier between the pad and the caliper piston, which can help prevent the brake fluid from boiling.