Religion-specific promotions are a must (and will be easy to implement in BtS, since the religion requirement was added for the Gods of Old mod). I can see there being several unique promotions per religion, but I'm not a huge fan of your specific proposals.
I don't see what command has to do with OO, or why necromancy should duplicate the effect of the Death II Sorcery spell (especially as it seems like a promotion that would best fit arcane units). I do like the idea of a necromancer promotion though, and the random revival of defeated units. It would also be nice if AV promos could give units extra bonuses on defied/hell terrain. Additional bonuses for their summons would be nice too.
I can't really think of much for the OO, but it should probably enhance ships somehow. I was thinking that letting OO ships get fear would be nice, then I remembered that ships are not living units, so this ability would be useless against your enemies navies. I guess they could always go with something more mundane like extra movement, withdrawal, or cargo capacity.
A nice Order promotion would be one that removes the religious attributes from defeated units (so they won't serve Hyborem in the afterlife) and removes religions from conquered cities. Allowing them access to the Blessed promotion could also work, but it would be kind of a waste since it it gotten so easily by spells and altars.
The leaves could grant access to promotions that have a chance to spread forests, a weakened version of subdue animal available to more unit classes, and a promotion that makes Treants likely to appear to defend a unit if attacked in the forests. The Woodsman III promotion could also be made FoL dependent.
Runes could get promotions that give units the ability to move through impassible terrain (peaks) or give extra defensive bonuses on tiles with mines or quarries. I also see siege units getting some sort of RoK specific boost, and the Guerrilla III promotion being made RoK specific.
The Empyrean (Lugus based) religion's promotions could offer bonuses against Vampires, increase a units line of sight, let units detect invisible, and maybe even remove the Hidden Nationality promotion from rival units.
The Council of Esus could grant access to the Hidden Nationality and even Invisible promotions (preferably with fairly high prerequisite promotions, to prevent abuse). Promotions that increase withdrawal chances and give additional first strike would also be good.
Difficult to attain religious-specific promotions which grant affinity to a mana type related to the religion (and possibly negative affinity to its opposing mana types) would also be nice.