I did not expected to see this thread so soon.. You really work fast
To the point: I like the idea of merging mages with conjurers and (a bit less, but still) tier 4 casters (by the way, still just 3 archamges? I think there should be a bit more allowed if summoners are gone). But I do not think there should be a strict rule: one spell per sphere level. It could be one good spell or two weaker or one normal, one with special purpose (lichdom & inspiration come in mind - basically one-timers).
That would also allow to reduce a bit the current number of mana types and we will get some room to implement dimensional & metamagic instead. 15 is too much, especially for a beginner - it is really hard to choose and the problem is much bigger than with separate sorcery & summoning lines.
As for the civ-special spells and unique spells for exceptional casters - great idea
Priests
I think that reducing their spells to just one school + healing is a bit much. At least give them ability to cast lvl 1 spells (loyality, courage, sanctify fit priests more than mages anyway). I never understood why they do not get channeling 1 - I have modded it and it works fine.
I think also that order priests should be able to use at least a bit of fire and AV to summon. Sun divine spells are too much on the offensive side, especially for the empyrean... (should be more defensive/counter espionage instead, or just give them spirit spells that go in that direction) I generallly do not like offensive spells on priests (Order & AV should be exceptions), better if they have support/buffing role.
Elemental magic
I think it should follow (more or less) the schema: 1 base spell (like them as they are), 2 offensive spell, 3 good summon (need to be balanced)
I do not like rust - it is not fun, and can't imagine rusted bronze, not to mention mithrill

Give us weaker crush instead
Water walk is fine, but rarely useful. So water sphere is a laugh beyond spring - on top of water walking the worst elemental. The second level should have 2 spells: water walk and a weak to moderate offensive spell (ice if ice sphere will not be in or acid based or just some kind of flood, tsunami is too limited and too sea-themed)
Alteration
I think it should have mostly buffs, debuffs and special purpose spells (terraforming, things like spellstaff, regeneration, hastur's razor) No summons except treants, and it is a good idea to make this spell divine
Necromacy
I do not use it much, but it seems fine. Lichdom as a death 2 extra spell seems great