I own both machines. They are both great but, if I had to choose only one it would be the 3200.
Why? Well, pdaxii13 (bug fixed pdaxrom beta 3) was designed for MicroDrive use especially the full version ones.
On my 3200 the SD slot is mainly used for removable storage and the CF slot is almost entirely devoted to networking. The 1000 has me constantly flipping between CF memory and networking. The SD slot is contantly occupied with one particular card and it is a major inconvienence to swap it out with another card so, I don't do that very often.
Have fun with your new Z no matter what model you choose.