GoZ Needs To Respect Polygroups - Currently when you use GoZ it destroys your polygroups. To work around this I have my model stored in OBJ format with all the polygroups. After I use GoZ I have to store a morph target, import the OBJ and then switch to the stored morph target state.
Importing A .MA File Does Not Carry Over Polygroups
This really limits the use of using the .MA file format. There are a lot of workarounds to get the best of the .ma format and still retain your polygroups, but this should just work right out of the box.