The aftermarket systems will "work" better...no doubt there.
My personal experience is different. The performance of my aftermarket system is vastly inferior to that of my original factory system. Even though I still have all the parts to my original system, I chose to go aftermarket for several reasons:
1) Through ignorance, when I removed my original system during disassembly, preparing to restore the car, I left all the components open to the atmosphere. Much later, I found out this was a no-no and probably ruined all the pieces - which would probably need to be replaced ($$$$) including the POA valve which is near impossible to find.
2) I built a fairly stout engine for the car and was concerned about having sufficient idle vacuum to operate the factory system.
3) I was concerned about being able to get R12 to charge the factory system, and research led me to the conclusion that converting an R12 system to R138a results in a much reduced cooling performance.
So, I went with an all-electric aftermarket system. No one made a plug-and-play system for my 69 GTO at the time (and perhaps still doesn't), so after completely striking out with Vintage (they were pretty dismissive and seemed to not even want to talk to me), I found a local supplier who was willing to try to help me assemble a custom system.
I was successful in that regard. My aftermarket system LOOKS factory, uses the factory vents, and the factory controls. I even managed to get 4-fan blower speeds out of it even though the system "really" only has 3 speeds, though some creative electronic hacking (I now have a "super" low speed that is below the unit's originally lowest speed.)
However, there are things about the aftermarket system that I didn't realize at the time, namely:
1) The unit operates in "recirculate" mode all the time. You lose both the 'vent' and 'outside air' modes of the factory system.
2) The air-movement capacity of the blower motor is just plain wimpy. Even on the highest speed, the volume of air it moves is roughly equivalent of "low-medium", maybe even "low" on the factory system. As a result, on a hot Texas day it can't keep the interior of the car cool. The best you can hope for is almost-but-not-quite tolerable. --- And this is even with the lap vents from the factory system not installed at all. I completely blocked off one of the air outlets on the aftermarket unit and am only driving air out of the three upper dash vents because I couldn't figure out a good way to connect the lap vents to the system - so you'd think this would cause it to push more air out of those three --- but it just doesn't.
So... one of these days when I get my new shop all fixed up and have the time to do it, I'm going to be pulling the motor to re-do the rear main anyway. At that time it's going to be tempting to revisit my a/c decision. Something's got to give - either I've got to find another blower motor with enough butt to move some air, find the as-of-yet undiscovered reason it doesn't, or give serious consideration to repairing and re-installing my original R12 system. I've since learned it's POSSIBLE to get R12 still, you just have to jump through a lot of hoops (exams, certification) to be able to buy it and it's very expensive.
As usual, your mileage may vary - everyone should make their own decisions, past results are not an indication of future performance, void where prohibited by law, etc.
This has just been my personal experience.