There were two turning points during the first generational run of T4R's. The change from carburators to fuel injection in 85 or 86 and the change in front suspension from a solid front axle to an independant (IFS) in 86 (I think).
Both of these are personal preferance, I like fuel injection and solid front axles myself, although I do like the IFS on my 90 (2nd gen) 'Runner.
The 22RE engines seem to last forever (4 cyl) and I really like the 3.0 V6 too. I have the 3VZE (V6) engine in my T4R and love it.
Personally, I don't like the auto trannys. I just don't like autos, but I DO like the shifter setup Toyota uses. The autos I have driven seem to be pretty good too.
The clutchs are hydraulic. You probaly understand them since you had an older MR2. Mine was dry when we bought the rig. I refilled and flushed it and it works fine still after a year.
On coil spring rear susupensions, the upper control arm has a tendancy to break the bracket at the rear axle. Any decent welding shop can fix it and you can get heim-jointed replacement arms for about $250 a pair. Coil rears also may sag a bit over time. There are replacement springs to fix this too.
The IFS torsion arms get weak if the front is cranked up to gain more height. Again, you can find replacements for these easily. The IFS is harder and costlier to lift, but rock solid if you like it stock. I do.
I have heard the clutch safety disconnect switch can fail and cause problems, but mine works fine, so I don't know for sure. I do know the dash switch for the rear window wears out and fails. Mine will only roll it up, not down.
Rust is a big issue. Mine is starting at the body seams in the door sills. A lot of them go in the rear wheel wells. I removed my mud flaps because they can hold water and dirt and cause rust too.
I've not really found anything else, but I am sure someone else can point out something I missed. Overall, very stout, good rigs. I love mine and am looking for another since my wife took the '90!
