Another thing I something consider when making a prophet, is making a profit.
IE : with some of the
really expensive non-sacred commanders, you can save a decent amount of gold by making it your prophet. This is especially important if you're going to have a bad gold income : for instance, Carrion Woods Pangaea. The Panic Apostate costs 320 gold, for an upkeep of 21. Making him the prophet, er, should halve that, but seems to make his upkeep 0, perhaps thinking he's undead or some such since he can reanimate undead. (Both base 2.16 and CB 5.2)