MOO3 didn't really follow the formula of the previous two games and implemented a lot of interface enhancements that were occasionally pretty neat. It rendered the 4X genre in a fairly unique manner, really macroized (made more huge and simple) the whole thing.
Unfortunately this also meant the 'personality' of the 4X games was left in the dust. It was hard to actually care about any of your planets, I always just went to the colony list, filtered for Industry primary and Population secondary, chose the top 10 - 30 planets and had them churn out the newest model of ship every ten turns or so.
But in a way that's what was good about MOO3, you were an epic space commander, you could control hundreds of colonies and many thousands of ships. Unfortunately the game was riddled with bugs which after a few hundred turns would sort of screw up the proceedings, IE, an enemy empire or your own empire could have its budget get too high/low and it would 'flip'. Sometimes my yearly revenue would go from a few tens of thousands, to a few TRILLION for no apparent reason..
And it was also riddled with unfinished features. The AI would not and could not invade planets. Cloaking devices and most of the whole ECM/ECCM feature on ships did not work. And this is after the most recent patches. The patches did help, they added some features and fixes, but didn't fix the above. The patches did allow you to better track the population stats of various planets, and also tracked things like what species your soldiers were. This could make certain planets more unique and compelling because for instance their population might primarily be a different race which had better soldier stats than your imperial race.
All in all I'd say the AI in MOO3 was completely arbitrary and it didn't feel at all like playing with another human. Really all you had to worry about was alliances and whether your relations were in the + or -. You had to send a new trade/research deal every twenty turns or so but there wasn't really anything more compelling to do with them. They didn't care about the current situation, and didn't care about the overall course of the game and what was going on.
Also the tactical combat in MOO3 was very... twitchy. Pretty much each fight I'd have to in the first split second choose all my taskforces which had missile-launcher ships in them an click on an enemy taskforce; or else, they'd fire all their volleys of big huge ship-killing missiles at either incoming missiles or incoming fighters. Absolute, total waste of their firepower. Making my taskforce navigate was also a pain in the ass, somewhat easier when I panned the view up for a total top-down perspective, but still.. trying to move a fleet of 16 taskforces in a fight was just a cluster-F.
The auto battle in MOO3 was also quite screwy. With a massive force of my missile ships against a decent number of enemy short-range ships, there was a huge risk of either losing several or many of my ships (impossible if I played the fight myself), or enemies successfully retreating which otherwise never would have. In GalCiv III, I trust to get a decently consistent results based on the power of the respective fleets. There's some close fights, but my ships do their best and it works out fairly.
Also I put hundreds of hours into MOO3 but never finished a SINGLE game.. it was too huge and took too damn long, and eventually I'd kinda lose interest. This wasn't the case with MOO1 or MOO2, and that's not the case with GalCiv II. Those three games are decently paced such that eventually, I realize it's time to pack up and end the game already.

To be honest the tech-tree doesn't seem all that long in GalCiv II .. but I don't think I've seen the end of it in any of the games I've played, so not =too= short perhaps.