Well, I'm a bit biased, since I'm one of the developers (for both GC1 and GC2), but I say yes.
Here are some of the reasons why:
1) The 3D engine makes a huge difference. Zooming in and out of the map, multiple resolution support (with more viewable area on the starmap for higher resolutions), and being able to change the angle.
2) Ship design, which would have been very cheesy and probably looked terrible on a 2D engine, works great with the 3D engine. It's very cool to build your own ship as if you were using Legos.
3) Fleet combat. In GalCiv1, fleets were more or less just a way to control a group of ships. It didn't give you any kind of tactical advantage in battles. In GalCiv2, a fleet of ships definitely has an advantage over a single ship, because each of the ships in the fleet fires before the other ship does. And the fleet combat window is really cool.
4) You can play as any of the major races, or create your own custom race.