This is a very controversial question. Be ready to hear just about every opinion in the world on this topic.
It all really comes down to what you can find, and how much $$$ you are willing to spend up front.
The first few things you are gonna hear about are the transmissions, brakes, and suspension. But here are the most important differences I can think of. I may be a little biased considering I have a '91.
Drivertrain:
-Transmissioin: The '91-'92 does not come with LSD. From '93-'95, it was an option, but it seems like more of them have it then don't. I have't seen too many '93+ MR2's without it.
-Fuel cut: The '91-'92 hits fuel cut @ around 12.5psi. The '93+ allows 16psi before fuel cut, but both have the same stock boost level.
Rollers/Stoppers:
-Wheels: The '91-'92 came with 14" stock wheels, while the '93+ came with 15's. Both have the same width and offset.
-Brakes: The '93+ brakes are bigger than the '91-92, providing a bit more stopping power. I've heard some owners claim the stock '93+ brakes to be the best in the business.
Suspension:
-Suspension: The '93+ suspension was altered slightly from the '91-'92 settings, mainly to correct the '91-'92 tendancy to oversteer. Although, many people hear don't find it to be a problem.
Cosmetics:
-Paint scheme: The '91-'93 paint jobs are usually found with the lowest part of the car being black, while the '94+ were usually 1 solid color.
-Front lip: The '91-'92 front lip is smaller and rounder, while the '93+ is lower and almost comes to a point. '91-'93' lips are black, '94+ are same color as car.
-Rear spoiler: The '91-'93s were equipped with a 3-piece wrap around spoiler. '94+ got a 1 piece, 2 pedestal wing. many opinions on these 2.
-Tailights: The most sought after (cosmetic) upgrade to a '91-'93. If you don't know the difference, do a search, and you'll understand why.
That's all I can think of right now. Please, anybody who finds soumething wrong with what I wrote, correct me. I'm no expert.
Like I said, the biggest determining factor will probably be price, and what you can find. '91-'92s are much easier to find, and are usually a lot cheaper. Next would be the '93s for rarity and price, and '94+ are the rarest and usually the most expensive.
There's lots of varying opinions on which year is best. You'll never get a straight answer. Many people feal you can buy a '91 and us the money you saved to upgrade the tranmission and suspension and be better off than just buying a '93.
As far as the cosmetics, you can always upgrade to whatever options you like, or downgrade for that matter.
It all comes down to what's important to you. I'm sure plenty of people will chime in whith their opinions, and you should listen to all of them. Gather as much information as you can and start searching. If you come across one you like, and it's in good shape, buy it. You can always change out the stuff you don't like later.
Best of luck
Frank