Hiho,
You did promise spells of great effect that will alter the world itself, here's what I consider strong magic 
- and, I find - an elegant solution to end game: Armageddon.
I'd like to see such a mechanism in the game - but not in the likes of archon II, populous, MoM (Spell of Mastery) or GalCiv (Research Victory)
I would prefer a way that makes endgame armageddon a goal to base one's strategy around during the game, and to make it not a one shot game winner but only nearly so. And to have a variety of.
Examples:
Base your nation (or whatever) around animating the dead. Become independent of living population. Reach armageddon through a plague killing all the living, creating dead to strengthen you even more. This will greatly harm anyone depending on the living, but not other necromants or others using inanimates as their backbone.
Become a nation living in the seas. Reach armageddon by flooding the land. This will strengthen you greatly and remove land dwellers from the game, but will also strengthen others living in the seas.
One single armageddon spell can therefore be enough to instantly win the game - But it doesn't have to. It's effects still would be very helpful - but will also help some enemies, maybe to a degree you don't want armageddon because it would help a secific enemy even more than yourself. (You are the weaker one of two underwater players)
And it should be obvious what you're trying to do, so players on the receiving end have a chance to stop you.