I recently bought and have been playing GalCiv II like crazy, however I think I still prefer Civ IV. I feel a lot of important points haven't yet been mentioned, although I'll also mention some of my favorite parts of both games (that already havee ben)
About SDAC (which I really consider a succesor to Civ II,) had the one thing that I REALLY loved, which was the unit-creation. Galciv II hooked and sold me on that.
I don't like how your power in galciv II is determined so much by the AI's heavy reliance on your military score. The galciv II AI usually fails to make accurate predictions about your production capacity, technological level and monitary state, regardless of slightly weaker military. The ship design, while nice for humans, really causes the computer problems when they can't design ships to keep up.
I think the civ IV diplomacy makes more sense, they won't trade new techs, for example (ie they want a wonder), but they're more willing to trade weapons and arms techs (just at a higher price).
I'm kinda usually miffed about how trading laser I is kinda useless when trying to trade laser II. I like that each tech is necsesary for future techs in civ IV.
Another thing that slightly annoys me about galciv II is it's combat system. In civ4 you DO NOT attack foritified units inside a fortified (castle when you have no gunpowder, for example) city on a mountain from across a river, unless you're prepared to lose a LOT of units. In galciv II the warfare is more attrition based, first strike is the only real strategic importance (for 1.1) and I feel it's going to be even more about attrition in 1.2. Combat units in galciv II also don't have enough special abilities (catapult/cannon/arty/offshore bombard anyone? ICBM anyone? fighter/bomber combat system anyone? collateral damage anyone? commando ability?) that make combat interesting and varied. In that sense I would like to see in galciv II bonuses (or perhaps ship modules?) that could you add to give bonuses against certain ships (oversized weapons, +atk to large/huge ships, fire control & tracking system: bonus against small/tiny ships, light AP rounds - bonus against medium ships) Starbases just add static bonuses to attack and defense right now, why not give them more interesting special abilities?
I also can't stand the offensive advantage in Galciv II. Perhaps defensive positions in space can't be rationalized, but I do like to play defensively (and I don't mean with shields on ships, I mean guarding my territory, planets, cutting people out with zone of control [ok so that isn't in civ IV, it's in SMAC, as well as the older civ games], etc.) and so I really appreciate defensive bonuses. In galciv II, planets are extremely hard to defend. shouldn't my ships be getting bonuses instead of me being forced to build an orbital fleet manager just to get them into a fleet? I was always of the impression a good (fortified) defensive position generally has an advantage, so long as the defender is not ambushed (by ambushed I mean caught unawares/by surprise) or flanked.
what I do HATE about civ IV is the turn limit... give me a break here, I just got all the cool stuff, I want to extend my game, play a little world war III, or IV, or V.... I can do that all I want in galciv II

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As someone else mentioned, it's almost impossible to be penalized in galciv II for overexpanding, not true in civ IV, forces you creature a more balanced empire. Bonuses also tend to all tie into the same or similar things in galciv II, whereas they have a much bigger impact on your strategy in civ IV.
I love the moral choices and alignments in galciv II. I see them as appromixately equal to civIV's civics, since gov't in galciv just give straight bonuses. Civ IV does have more choices in this respect, but galciv's is interesting in that you have to balance what you want (although right now it's not much of a choice right now, neutral or evil, with neutral prefered).
the built in civilopedia makes newbies happy. we are all newbies at one point, and it was a feature that was sorely missed when I was trying to figure out the benefits of each tech (ok sure, I get laser IV, how is this better than laser III? smaller? costs more or less when putting it on my ships? does it do more damage? What am I GETTING for god sake?!?!?!, yeah, I know it's laser IV, big whoop.)
managing logistics in civ IV (roads) is a bit more challenging and important than in galciv II, as is resource management (yes, you need iron and horses to build those knights. Can't mine it?, better have good diplomatic relations.) As of right now good dilpomatic relations only give you an edge in trading
I've always like how barbarians in civ IV will give you trouble early in the game, it makes you keep your foot on the military. (I'd like to see more pirates, etc. in galciv II, even rebel faction/dissident invasions, not just defections.) I like how galciv II wonders are never obsolete

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Overall I'd have to give civ IV the hat, due to it's extra depth. That is, after all, why I play 4X games isn't it? strategic depth.