They both have their problems.
Mk3 deficiencies:
- The Mk3 loses head gaskets due to lack of torque on the headbolts from the factory.
- The Mk3 is too damn heavy, and moving to a Targa instead of a sunroof was a stupid idea.
- We lost the interior flashlight and the under hood integrated trouble light, too.
- The digital dash in the Mk2 was available in LHD, unlike the Mk3.
- The design of the shifter boot on the Mk3 is weak sauce by comparison to the ones on the Mk2.
- The W58 tranny from the Mk2 is smoother than the R154 found on the Mk3.
- I've blown up the 7M engine twice.
- Interior door handles suck. Badly.
Mk2 deficiencies:
- Mk3 has better suspension.
- The Mk2 suffers from rust HEAVILY - far more than the Mk3. And yes, I'm still comparing apples to apples here, I've owned several Mk2s in the same age range as my Mk3 is now, and all from the same area, so same driving conditions, salt, rain, etc. I've had a Mk2 rust out on me completely, to the point that the rear shock towers collapsed!
- There are way nicer 5 bolt rims available than 4 bolt rims, and trying to upgrade the Mk2 to 5 bolt is a pain.
- The instrument cluster on the Mk3 is nicer.
- The R154 transmission on the Mk3 is tougher than anything found in the Mk2. Same for the rear diff.
- I've blown up the 5M engine three times. I've also been driving them for twice as long, so this may not really be a deficiency, I guess.
- Exterior door handles suck unless you get the 84+ variant, the earlier ones are made with something that looks like plastic and it about as tough as almond roca.
However, they are both dead sexy.