Some of it can come down to what you want to do with the car as well. I've had a gen 3 for something like 6 years now and 80,000+ miles and I love it. The gen 3s were easier to tune back in the day since an SCT worked on them, though I guess the gen 4 ECU just recently got unlocked so it can be tuned as well. Not sure what all goes into that though, so it might be a bit more complicated than a handheld tuner. Chassis wise I believe they are basically the same. Same suspension and geometry I believe, so there shouldn't be much difference in driving dynamics. The engine would be the biggest change, though if you plan to rebuild it anyway I'm not sure if starting with one over the other makes a difference. Interiors are the same as well, so you wouldn't see a big difference from the inside either.
The short version of the story is anything on a gen 4 can be put on a gen 3, so if you are planning to modify it anyway it might make more sense to start with that as a base. You can always put a TR6060 in when you rebuild the motor. The T56 will put up with a lot of punishment if driven right. The rear end I'm not sure I knew enough at the time to compare. I ended up swapping in a gen 4 unit because mine was making a bit of noise after an incident I had, so I figured if I was going to replace it then why not upgrade? It was cheap enough as I swapped my gen 3 core and a few hundred bucks for a used gen 4 setup. I hear the gen 3 units don't like excess power as much, but I can't really speak on that as I'm mostly stock power levels.
I guess I'd say add up what exactly you think you want to do to the car and see where you end up. It might be cheaper to buy it all at once in a gen 4, but if you think you want to start stock and start modifying later then it might make sense to start with a gen 3 and add on gen 4 parts as you up the power level. It could potentially be cheaper if you shop around.