Here's my take. Mk4 you get more creature comforts like heated seats (unless you get a mk3 glx), remote entry (can be retrofitted on a 3), newer gadgets and a cooler interior. It would probably be more comfortable on a long haul or daily routine than a 3, however they are more expensive to mod and things like to break more than on a 3. Mk4's tend to have issues w/ the brake switch, door lock mechanism, window regs, maf, and rear brakes. Thats all besides all the normal vr6 engine stuff that will happen on either generation (waterpump/pulley (if you are going to s/c it), chains (after 100K), thermostat housing, coilpack and crack pipe) except the mk4 also has bushings in the manifold that need replacing over time.
The Mk3 models have less issues overall and you pretty much just need to worry about the normal vr6 quirks previously described. I have not had any issues with mine beside the thermostat housing and the waterpump pulley (but this was because of the pressure the blower puts on the pulley).
Performance wise the mk3 WILL be faster, and has a better blower available (v1/v2 instead of the v9 on the mk4's). Obviously you can get a 24v in the Mk4 and s/c it to make it pretty quick too, however its going to be a bit more expensive, harder install and you get to deal with the lovely 02M 6speed tranny. (02M has the clutch slave cylinder built inside the bell housing which makes it prone to failure easier and requires replacing the clutch when it goes because it leaks all over the clutch disc).
Personally my choice is mk3. I went from a mk4 to a mk3 and while I do miss some of the creature comforts my mk4 had, the 3 is more fun to drive, and has less issues.
I do see your point about the less miles, but if you are just going to be racking up the miles on it anyways, get one that is less expensive to start with and would be easier to maintain.
