Safri

What you could do is 'loan' your units to an ally. I think Hearts of Iron did this. It would basically allow you to give your units to your allies to control, so they could do what they liked with them, but you could recall them at any time. Would stop your own units turning on you.

For the fog of war, what about making explored land a certain distance away from you fade back to black/undiscovered until you discover a technology like mapping/map making, after which it would just be obscured by the fog?

The thing with infinite resources is that they lead to a more aggressive tactics and involve less strategy. If you know you've got resources to build another army straight away you can just throw waves at the enemy. Finite resources might lead to a player being too cautious and defensive if there's not enough resource in the pile, but it makes them more likely to think strategically about what they're doing. Finite resources, with a decent amount per source would be the best way to go I think, a kind of a balance between the Age of Empires system (which often ran out too quick imo) and Empire Earth (basically infinite except for wood).

What about if you have something like in Civ 4, where there is a small chance a reasource can appear? It could reappear and you get a message saying "we have discovered a new source of stone" or whatever?