It really is a hard decision mate. I was in the fortunate position where I had access to both due to me handing the reigns of the MR2 over to my Wife for a while. I don't regret the trade for 1 second but there is nothing quite like getting behind the wheel of a nicely tuned MR2. Mine was running around 280hp and it scared the pants off of all my mates. The Supra does the same but in a completely different fashion. The Supra is refined, comfortable, easy to drive, smooth.... the MR2 is none of those things and feels completely raw.
In a perfect world I would still have both to be honest. The Supra would win 9 times out of 10 when it was a choice of which car to go out in but I can assure you I would grinning from ear to ear everytime I chose to go out in the MR2.
As Johnny says you can't take the MR2 very far unfortunately. I would say that around 350hp would be the maximum for keeping the car as an "all rounder". A 300hp MR2 will have similar performance to a 400hp Supra below 80, in fact in normal road going guise I think the 1/4 mile times would agree with that. They are very nimble machines and great fun to drive but the Supra is just a more superior car in almost every way.
At the end of the day I wouldn't recommend spending a lot of money on your MR2, it will be money down the drain. Buying a TT6 and having it at BPU will hold reasonable value for whatever length of time you decide to keep it (within reason ).
Happy hunting
Oh, check out my garage