Well, since you likely have the two pack, why not try both and tell us? Beyond that, it's different strokes for different folks.
Personally, there's a lot of a little details and ambiance I like with Moo2. Custom races, leaders (heroes), boarding actions during battle, the music, more starting condition variables, space monsters, and much more. I've had a lot of good times with the game. Then again, I always found the colony improvement system to be tedious in larger galaxies, especially when playing a "creative" race. Drilling down to all those colony build queues to add yet more additions gets tiresome for me. Again with larger galaxies and higher difficulties, the big scale battles can get a bit tedious too. When I load up Moo2, I tend to stick with small and medium galaxies these days.
As for Moo1, I really appreciate the purity of the game. Some of the colony management tedium is eliminated by the "simple" slider bars, letting you focus on grand strategy and battles. Which, in my opinion, is the real meat and potatoes of the game. I also like the more randomized tech trees in Moo1. With Moo2's tech tree design I'd usually find myself slipping into the same set research path most times I'd play. With regard to combat, due to the way ships are grouped, battle tends to be more straightforward. Large battles are less tedious, but also less tactical.
Not to sound like a diplomat, but I think the best choice is simply playing both depending on whims and mood at the moment.
How's your first campaign going, by the way?
Post edited July 06, 2013 by Nomad_Soul