One bit of magic I'd like to see in this game, that seems to fit with the whole epic theme, is the ability to levitate fortresses or even entire cities into the air.  Kind of like Miyazaki's Laputa, or like Moon's Spawn from the Malazan Book of the Fallen series for those who have read it.  Presumably this would take a rather large amount of magical power; I can even imagine charging the player to levitate it in the first place, charging an ongoing upkeep to keep it in the air, and charging to bring it down or to move it around.

This would have all sorts of uses in the game, for instance:

1. It's cool.
2. It could protect a fortress from enemies who don't have enough magic / tech to assault it (by flying up to it, conjuring a magical bridge, cancelling the levitation and bringing it crashing to earth...).
3. If zone-of-control is a factor, floating fortresses could control more land due to the better vantage point they enjoy.
4. It allows use of the ground under a city as extra building space.
   
5. It would presumably greatly increase the culture / influence of the city, because a flying city is just that cool.
6. A tower could be filled with units and (presumably slowly) floated over to your enemy's stronghold, from where it could be either planted on their doorstep or even flown straight over the city to RAIN DOWN DESTRUCTION FROM ABOVE.  (archers, magic, boiling oil...)  Heck, they could even just bring some big boulders up and drop them over the edge.  Or maybe magically parachute right into the middle of the city, bypassing the outer defenses, and proceeding to wreak havoc.
7. If you try #6 and don't defend the tower well enough, perhaps your opponent could capture it and turn it right back at you.
8. When you have your massive death-dealing fortress parked above a hostile city, it seems only natural that it would have a massive effect on loyalty and morale, for pretty much the same reason that capital ships do in Sins of a Solar Empire.
9. Maybe there would be some tourism bonus to the economy for having a floating city?  Makes sense to me.  They are pretty cool; I'd want to go gawk at one.
   
10. I like the idea of being able to abruptly cancel the levitation, bringing the whole structure crashing down onto whatever is beneath it (armies, cities, ...) and of course killing any units that are along for the ride and turning the whole thing into a pile of rubble.  Presumably the game should be balanced so that this is normally more costly to the player who invokes it than to his opponent... (either by including countermeasures or just by making the floating towers really expensive / hard to create)

Other ideas I thought of:

1. Maybe it should be hard for the player to move units up / down; so for cities that are "parked" you'd want to construct a permanent bridge / ferry terminal to transfer units and allow trade to take place.  This would then become a target for the enemy, either to destroy it (cutting the city off from trade, food, etc) or to capture it and use it to gain access to the city.
   
2. A large floating structure would block out the sun beneath it, like the floating cities in Ringworld did.  This could be used to inspire terror in your enemies, or as a way of indirectly ruining their crops.  It also would limit what you can use the land beneath the structure for.
   
3. Floating structures are cool.  Did I mention that?
4. If floating structures can move around, maybe it should take higher-level research to do that (so at first you can just raise something up to build underneath it, and later you get the ability to move, maybe with extra research to move faster).  I could also imagine requiring more research to levitate a large structure (say, a whole city) than a smaller one.