I should start out by stating that I really prefer MoO (1 or 2) over GalCiv 2 and this post may end up sounding like a collection of gripes about the last. Also, I don't have any of the expansions for GalCiv2 and those changed some things.
GalCiv 2 is the best looking of the three, though I've always preferred the cartoonish look of the races from MoO 1. (The Klackon ambassador looks so happy when you establish trade.)
It's been some time since I've played, but from what I recall the GC2 interface is well laid out and there's a number of features to make running the empire easier, such as changing what ships are being built (ex. all planets that constructing transports should stop building, everyone building Yeoman-class ships should start on Archer-class, etc.) and where their muster points are.
There are a lot of diplomatic options in GC2 - you can (on either side of the deal) include technologies, planets, ships, money, votes in the council and status changes (peace, alliance, etc.). Diplomatic skill comes from racial bonuses and research; the higher your skill is compared to the other guy, the easier it is to get him to accept.
Alliances are actually groups, not just pairs. In MoO, the Psilons might be allied with the Humans and the Alkari without the Humans and Alkari being allied. In GC2, you would have an alliance of all three races - this means that everyone in an alliance has to agree to let someone else join.
The United Planets meetings are sort of half nuisance, half diplomatic opportunity. Some of the resolutions can alter the situation greatly, but it's not like the council in MoO1, which can be a real threat (in theory, the one in MoO 2 could be as well, but that's somewhat rare).
The AI is generally pretty good and doesn't cheat unless you set it to the highest difficulty levels.
GC2's production and research system takes a bit of getting used to. Basically, your factories and labs represent potential for production or research, but must be funded to work and higher output takes more money.
I note at this point that I loathe Industrial Sectors, which are supposed to be the "best" factories :P
Unlike MoO, you can't really have early wars in GC2. Ships can't hurt planets and "Planetary Invasion" is a tech you have to research. Invasions are carried out by transports, which you have to build (like in MoO2) but which take population from a world as "troops" (like MoO 1). Planetary defenses are either ships stationed on the planet (in orbit?) or intercepting enemy ships before they reach your worlds. There's a limit on how many ships you can have on a planet (maybe 8 or 10, it's been a while). These fight the attacking fleet one ship at a time.
Fleets have their size limited by logistics points - bigger ships use more points. The battles play out automatically; you don't get to control your ships. OTOH, there are no unusual weapons or devices (teleporters, cloaks, transporters, etc.) so it's basically just a slugfest.
As noted above, ships can't hurt planets, so if you want to actually hurt the enemy beyond destroying his ships you'll have to invade his planets. I always missed the MoO ability to simply bomb hostile worlds, whether to soften them up for invasion, weaken the enemy empire or just exterminate the colony.
Ship design is rather interesting in two ways. You can design the appearance of the ship but starting with a base hull, then adding parts to it - extra structural bits, lights, towers, etc. The actual abilities come from weapons, sensors, engines, etc. that you mount on the hull. Offense and defense are of three kinds - missiles, beam weapons and mass drivers, each with its own defense. These defenses work best against a specific attack (armor vs mass drivers), but still provide some protection against the other two types. Ideally, your ships will have defenses against the weapons used by whomever you're expecting to fight and an attack that they haven't researched a defense against. The AI will research or trade techs so as to counter your ships, though.
Research is usually pretty linear - you'll research say, Lasers I and then on the Lasers II (same damage, but take up less space). Most of the ship-related research will be like this, whereas the rest tends to be more on the order of +10 to your diplomacy or giving you a better structure of some kind (labs, factories, banks, etc.). You can jump ahead by trading for or stealing higher level techs - if you have Lasers III and trade for Phasers I, you could start researching Phasers II (but you will not have anything between Lasers III and Phasers I unless you research those).
There are a number of different victory conditions. It's possible to win the game by getting everyone into an alliance, though it isn't easy and usually "everyone" will be "everyone we haven't killed off." You can also win by cultural influence, technological mastery that leads to becoming energy beings and of course, you can just wipe out everyone else.
Hmm - that was mostly about GalCiv 2, but it sounded like you've played MoO but not GalCiv.