The A1200 has two advantages as I see it. For one, it is a lot easier to get a USB solution working in an A1200.
I have never been able to get my Subway working on my A4000 despite having tried it with clockports from an X-Surf, BuddhaIDE, and Kickflash. None of them work.
But if I put the Subway on the clockport of my stock A1200, it works perfect! I've had basically the same experience with the Delfina clockport, though at one time I did have it working off the BuddhaIDE.
I also had a PCI USB card working on my A4000 at one time, but that has since quit working also.
So, just basing on personal experience, its seems USB is much simpler to implement on an A1200 vs. the A4000. Just IMHO.
The other reason is the amount of RAM that is suported: A4000 with a CyberstormPPC, the Max is 128M, whereas an A1200 with a BlizzardPPC can use up to 256M. Otherwise, Flashlab is right: Z3 is a better performance, but with PCI..who cares?