I actually like Moo3 post code patch for one set of reasons while I like Gal Civ for a variety of other reasons. It really depends on what mood I am at the moment.
Moo3 pros: backstory, ship design, complexity, graphics (except for combats), special situations (guardians, New Orions, the Harvesters)
Moo3 cons: AI castrated (has improved), space combat, UI a bit on the clunky side, LOOOOOOOOONG patch cycles
Gal Civ pros: AI (I find faults here and there, but its still good as a whole), diplomacy (viable here), much more rapid bug fixes and support, generally tidy UI
Gal Civ cons: Memory leaks, very long load times on large maps, sound effects seem cheesy
Overall Gal Civ is a better game than Moo3 in many areas, but I like the two as I said for differing reasons, though I've played this game through much more than moo3