I've never played MOO3 either. From what I've heard, it was hard to manage certain aspects of the game because they automated too much and certain game controlling elements were deeply hidden in sub menus. It was a design decision to try and limit micromanagement, but either they implemented it badly or they went too far with it. But as I said, I've never played it, this is just hearsay.
MOO2 is a good game, but the AI in that game is pretty poor, especially concerning designing capable combat ships. I've also played it a lot, but now consider it a game that is fairly easy to beat even at the highest difficulty level.