My favorite spells from MOM (which haven't been mentioned in the OP) were Time Stop and that "raise zombies everywhere spell" which IIRC Armagendon(?)
Timestop was awesome game winner spell what would happen is you cast Time stop and only you can make moves, oppenents you attack can fight back but they may not move on the main map. In addition nobody produced food, products, research or Mana. And cost you a shed load of mana a turn (i think about 35). Anywho it was such an Awesome spell.
The zombie creater spell was even cooler basically every fight you won you got zombies back from the dead (from your fallen commrades) and in addition hostile zombie mobs spawned throughout everybody else's land.
I really like the sound of the contextual spells like the freezing river. Though I think I would prefer being able to use fireballs to kill soilders/peasent, burn down vilages (targeting buildings), crops and perhaps melting galaciers or evapotaing water sources.
As for creating diseases that would be cool and from a gameplay design point of veiw, having them affect species(or even better individual subgroups within them, so that I as a human could create a disease to kill other humans whilst being immune to it) does make the most sense. Its not strictly speaking true it would depend upon each individual disease and its source (whether that be virus (most specific) or Bacteria (much less specific). And on top of that with them both the Human and the Fallen being very closesly related its hard to imagine that they be affected by a competely differnt set of diseases.
*But i think a super complex disease models working around pathogensisty factors vs Host defence factor, taking into account the individual condition (both poir and throughout the disease), modes of transmittion, evolution and resoivour of infections. Would be beyond the scope of this game. And i'm bretty sure if somebody could generate a model taking into account these type of factors you'd probably find it indemand from numerous scientific intestutions and a bit too complicated for Elementals target audeince (no offence).