your idea is similar to what i loved about the original starcraft!!   My bro and I would spend hours playing as the same team against the ai and just have sooo much fun.

There is a very big difference thuogh....  RTS vs TBS.   In an RTS you're always against time trying to get everything done, in a TBS, you have all the time in the world to organise your tactics and make sure that your overall strategy is happening on the various sub compnents (research, city building).

Perhaps an approach like World at War might make this doable, ie, lock down what each player can control in regards to the empire, rather than the star craft approach which was you could both control everything.  Perhaps one player controls Armies, and diplomatic relations, and the other player controls research, cities, taking on quests.   I can see on eissue in this solution though, end game will have one player getting a little bit bored because all cities are upgraded (although micro managing could make up for this (changing buildings based on what status of game: eg shift to research during peace, shift to production during war).  Perhaps the best thing to do is allow all control and just pick carefully who you play with?

Could you find someone you want to play coop with that you think won't destroy your strategy?  Will work well together and not always do the same stuff as you were doing?