AT FIRST: sorry for bad english and spelling mistakes
I've drove both... RX-7 FD3S and a MKIV !!
I really like both cars. And every car is a beauty for its one.
Difference:
The MKIV is a GT Car. This car is a highway killer. Top Speed is the best discipline. You can drive every day with the car and have enough luxury.
The RX-7 is a absolute Sports Car. This car is a road and motorbike killer. The RX-7's home is the track. The RX-7 have a very low balance point. It's a really FUN-CAR and my opinion is: It's no and never a daily driven car.
Engine:
The MKIV Engine is the most better one. Rare engine damage, but if you have one, you should have a much of money. A little bit economy fuel usage, easy to tune for 400HP and more, no temperature problems. Much more lag at acceleration, typical Pistons Engine torque.
RX-7 engine is a little bit more poisonous, engine damages are not a rarity, but a complete engine rebuild costs not more the 2500 and you have really fun for the next 60.000 - 80.000 miles. Much fuel usage, much temperatur problems. The Twin-Turbo System with a rotary engine is ingenious. Torque like a dieselturbo engine and this power from 2x654ccm.
Result:
Buy both !!if you have the money.
MKIV for fast and easy daily driving and the RX-7 for fun, trackdays, quatermile etc.
My opinion at the moment:
I look at a Supra MKIV TT 6Spd but must check my finances first and sell my old daily driven BMW E36
At moment my fun car is an RX-7 FD3S with a lot of mods and i have build rather a showcar than a trackcar. I like the combination.
But if my BMW was sold i definitly buy a 6Sp MKIV TT and can be lucky with both cars.