If you don't mind space fighting and dated graphics, look for the Homeworld games. They are masterpieces. Well, except the first ones expansion

If you do mind the graphics, look at Sins of a Solar Empire.
Also as someone already said Supreme Commander is good for large scale battles, but you should get it's standalone expansion Forged Alliance instead, it has many good improvements, and you won't miss much on the stroy department. Supreme Commander 2 is a good choice if you like the first but feel it's too slow or cumbersome
