I've been thinking on a magic-system for my WH40K-mod and recently I got an idea I like. The tricky part is doing something the AI have any chance of understanding naturally. I figured I could use the Promotion-table and have some magic-like abilities, then block them somehow (maybe setting tech-prereq to something you can't get) so you can't get them by levelling up and instead award (preferably give option to select like the normal promotions) them to units some turns after they're built and the abilities are "used", then also set an expiration-timer before they're removed from the unit. It should then work like a normal fantasy magic-system (gain mana with time, use mana on spells, spells time out). Then hopefully the AI will use them as intelligibly as it picks the normal promotions.
Religion and alignment? I'd love to have that in WH40K too. Perhaps there are some functions that affect how much the AI-player likes you and you can just fire them whenever policies and techs are adopted. Religion, again probably best to give with policies and techs and just let it spread around and do whatever it does without having too much of the impact based on the player's action because the AI probably can't take advantage of it.
I saw in a Dragonia mod-thread you had a magic tech-tree. There are many ways to completely separate tech-trees in Civ 5... Since promotions can have tech-prereq I think it could be nicely motivated with a separate tech-tree for the magic-promotion I mentioned up there.
Another slightly random thing, there seem to be an unhappiness attribute for the unit-table. I was thinking calling Happiness "Purity" or whatever then have certain units like Daemons only give that unhappiness. It also seem very fantasy, just mentioning it in-case anyone can expand on it. It wouldn't be that fun with something that's identical to happiness in every other way but this.