Give me a break. 

This thread is nearly pointless as you are asking for an opinion. 

GCII has benefited from 10+ years of DLC and 3 major expansions. Come back to this game after 10 years and ask this question again. GCIII is FAR better by light years. Native 64 bit, Hexes, Adjacency bonuses, Better ship designer, Better color and textures, Minable strategic resources, Improved Diplomacy screen, the list goes on and on. 

Of course GCII may feel better to you, however the AI  in that game can NEVER improve, here in GCIII it is data driven meaning with time and mods this game will likely end up the very best 4x in 20 years. 

Cheer, 

A good 4X matures over time like a fine cheese, as long as it is looked after.  It's a tad unfair to compare the two at this stage.

not counting espionage which two does better. Three has the planet list in your face. Better battle viewer. Ship designer is a moot point. Better star bases. Better resources. More types of resources. Adjancency bonuses. Upgrading on each step. The tree broken up. Specializations. In your face Ai. Potential for more players. Pirates. Bigger maps. More stuff in spAce. Different starting positions. At least gives you pictures of resources. Idealogy.

two has the ability to upgrade not destroybuildings. Two has trade goods instead of tradeable resources. Galactic achievements. More starting players. More customizable starting players.

I think three wins. I like both games.

two came out on cd with the ability to register so you never lose the game. If you don't have the internet you could at least install the game. Two had a digital and paper manual. Two had an editor for non modders. Does diplomacy do anything in three. Still think three is better.

two had minors building star wars. Three has 10000 minors. Three has better diplomacy looks. The menu system is better in most ways untill in need to organize planets.

GalCiv III is a better game but GalCiv II has a lot more depth.

Galciv 3 over all is better: 

1) Ship Designer is much better in 3 than in two except it needs better ways to organize ships and ship hulls like maybe an option to organize by class etc.  Also would be cool to be able to copy a design in the designer and PLEASE add a way to delete hulls in the designer.

2) The Battle Movie is better as well as having the ship class system.

3) Bigger maps - Still waiting the  Immense map  to be activated in Multiplayer (please)

4) Pirates - Also waiting for these to be activated in MP.  However I would also like to see more baddies like this (Antaries Attack anyone)

5) Better custom race designer - Still waiting and a way to attach specific custom ship styles to custom races such as Borg ships to the Borg, Cylon ships to the Cylons etc.

6) There are more but I can't think of them at the moment.

GalCiv 2

1) GalCiv 2 does have a more 'complete' feel to it but this is to be expected since Galciv just came out.

2) The bad guy invasion events which was really cool especially when they appeared while your still in primitive mode. The scramble to defend your empire under this pressure was awesome.

3) Galciv 2 was better organized like listing planets by alphabetical order, See all the Ship Fleets and put them in order od name oe power or def etc which is the same for other features in that game. GalCiv 3 desperately needs this especially since it is a bigger game with bigger maps and more planets and ships, Starbases, and ship yards to manage.