First, let me remind everyone to be polite. If someone's disappointed in the game that doesn't mean you get a free pass at trash talking.
population-based effects
I'm not exactly sure what you mean, but if you want to do things like population adds production, you can do that.
rewiring the whole magic system:
spells researched rather than obtained on level-ups
Yes
magic levels contributing to spell power
Yes
overland spells needing (variably) several turns to cast
This one might be tricky. It works as long as it is your sovereign doing the casting. If you use other units it starts getting messy.
a resource governing how much mana can be used per turn
Yes
technology tree
Yes
