If Zack was incompatible with Jenova cells he would have made a terrible SOLDIER....
Sorry, I meant to say S-Cells, but that wasn't really coming to mind when I was thinking about it.
The problem was that Genesis couldn't use Zack's cells because as a SOLDIER his cells had already adapted to Jenova matter, so the "S cells" Hojo put into him were bonded to his already Jenova infused cells. Genesis and Hollander assumed that Cloud's were just kind of lying dormant in him, so they would be usable. And it wasn't just the cells, Zack also got a lot of extra mako from the procedure, powering him up more as well.
Ah, lol.
Dammit, I've had it backwards for such a long time, now. Thanks for clearing that up for me.