More thinking out loud than anything, but the following are some ideas for other specialized casters of various sorts.
Swap ability to make potions, constructs, and crossbreeds for the ability to turn/control undead at first level and the ability to create sinkholes of evil at 11th; tie this latter ability into sanctum construction somehow.
Make death, healing, and protection spells easier; blast, illusion, and movement spells harder.
In my Eíre setting, necromancers are criminals, allied with Chaotic forces.
Break the class-building rules a bit - build as a thief with 1d4 hit die, and swap out all of the thief skills for spell-like custom powers at the various levels. The end result should look like an inflexible mage who can spam magic missiles.
In my Eíre setting, war wizards would be mostly from the Summer Empire; exotic and feared, but with powers that are reasonably well known.
Base bonus repertoire spells on CHA instead of INT.
Potions are cheaper and faster to produce ... but have a limited lifespan. Maybe call them herbals.
Scroll spells are a little cheaper and faster, but are stored in a familiar instead of paper - can't be traded to others, and require the familiar on hand to use. On the other hand, not as bulky! Maybe add a proficiency that gives the familiar a thief's chance of using one of its own scroll spells on the mage's behalf.
Swap constructs for elementals.
Swap crossbreeds for the ability to craft permanent curses of some sort on a region, family, or political group.
Make summoning and transmogrification easier; make blast and death harder.
Require a sanctum to be in borderlands or wilderness.
In my Eíre setting, when a primitive group has a special unit with 1d4 mage levels, I would swap out witch levels. Human witches would be rare - civilized wizards prefer blast spells and constructs over hokum.