MOO2 had space monsters. That speaks for itself.
Sometimes, random wandering space monsters would attack a system. Or even the dreaded Antarans would send a small force to wipe you out (or an AI empire). Space monsters guarding a system usually guarded a planet with something interesting on it. Could be a pirate cache for some quick money, an abandoned colony that you can resynch with and get free pop, a planet inhabited by primitive natives that you can add to your empire (they could only work as farmers, but were good at it), ruins with techs in them, or other interesting things. Far more interesting than SEIV's boring ruins system.
MOO2 had a better combat system. There were shield facings, movement costs to turn, much more interesting devices to add to your ships (a device to randomly spin an enemy ship, a device to place an enemy ship in a stasis bubble, devices that would do damage on the next few turns to a ship, etc.), devices that let you fire weapons twice a round, in-combat cloaking devices (though phased cloaking + whatever the temporal device that let your ship have an extra turn, every turn, was extremely unbalanced), a vastly superior mount system (more variables were affected, and you could apply more than one mount to a weapon, so long as they were not of conflicting types), etc., etc., etc. Unlike SEIV, MOO2 had an initiative system. Initiative was mostly determined by ship speed, but there might have been a few small factors that played into it. I forget. Anyways, the ship with the most initiative would act first in a round, regardless of which side controlled it. Unless you had a significant advantage over the enemy (or disadvantage), you would generally see a few ships on one side move, then a few on the other side, then a few on the first, and so on.
The tech tree was somewhat boring though, as there were only 8 or 10 tech areas (I forget how many) that represented general fields, such as Physics, Propulsion, Construction, etc. You would research these over and over. Each level had a different name though, and they had an interesting system where you could only choose one item from each level (unless you had the creative trait). The other items could then only be acquired in trade with other races.
Race design was roughly on par with SEIV. While the basic traits were less detailed (choose -1, +1, or +2 in an area or somesuch rather than SEIV's percent system), the advanced traits were often more interesting. They were often more far-reaching in affect. I don't remember most of the specifics, but a google search will probably find a MOO2 fansite...
Of course, capturing enemy races was far, far more interesting in MOO2. They actually retained their native abilities, not just magically functioned as your own people do, save atmosphere. There was also no atmosphere as in SEIV. Instead, each planet had a different type, such as irradiated, rocky, arid, terran, swamp, etc. This applied equally to all races, except Aquatic races. They treated all planets with water as one class higher than normal.
The diplomacy model was more functional than SEIV, if less detailed. The AI actually did what it said it would in a diplomatic agreement. Usually.
The AI in MOO2 was no better or worse than the SEIV AI. Neither series has ever been known for its AI...
Systems in MOO2 were less detailed than SEIV. No storms, though there were real asteroid belts (which you could eventually build artificial planets out of, or create by blowing up enemy planets).
You could not move in a system, only between them. All ships were just in a system or in transit to another system. There was a maximum of 5 or 6 planets per system. They planets actually orbited the stars and rotated though, so that was nifty. Far better than GalCiv though, as different races could occupy the same system. Planets had a type (irradiated, barren, arid, swamp, arctic, terran, etc.), value (not in percents, but more finite quantities), and size. Somewhat like SE4, except that any race could colonize any planet from the beginning of the game. Not all were very useful to colonize for a long time though...
Planetary management was more detailed. Each unit of population was specified as being in food production, resource production, or research production. This lead to more micromanagement in the endgame though. Going back to the racial traits, the basic ones, like food modifiers, would affect how much food each unit of population produced. Facilities generally modified what the poplution produced, or how fast it grew, or were defensive installations (fighter pads, missile silos, troop barracks, training facilities, etc.). All facilities were buildable on all planets. Production was not limited by number of facilities, but rather by population (and planetary value). Population limits depending on size and type of planet. You could terraform planets to improve their type.
Sadly, MOO2 was never made moddable...
That's probably enough for now.
My oh my... how could I forget these last two?
MOO2 had leaders! These were either system governors or ship captains, depending on the leader. You could only have 4 of each. They naturally provided a bonus to the planet they were on or system they were in, or to the ship they captained or the fleet they were in.
MOO2 had that often requested feature where you need special facilities to build larger ship hulls. You would have to build a space station or battle station to build the larger ship hulls.
And one more thing about techs... MOO2 did not have levels of components. There was just Laser Cannon, Plasma Cannon, whatever. However, when you researched a more advanced level of the area that gave you that weapon, the obselete items would be miniaturized a bit. So in essence, there were levels, where the more advanced ones were made smaller and smaller as more tech was researched (up to some minimum size).