Aight, so MoO (4?) plays a bit more like Sword of the stars with it strategy map, tactical map separation.
Combat can be played either in real time or turn based (where it just automatically pauses the game every set amount of seconds, you can also pause it by yourself if you want to.)
In MoO combat you can affect several things, you can choose targets for your ships, order them to move, decide what weapons to use and change around the engagement ranges as well as at what range the ships start fleeing the enemy ships.
Strategy map is flat, while in Sots it is mostly 3 dimensional.
Also, unlike in Sots here all raceshave same FTL system and all use jumplanes or jumpgates in later game, this does make picking colony locations a bit more of a strategic thing than in Sots (unless you play human vs human games there).
Designing ships in MoO is significantly easier in than in Sots.
While in MoO you just pick a ship type and then pick what weapons and or modules to put on it, in Sots you choose what action section the ship has (mid section), what bridge it has (forward section) what sorta engines it has (aft) and then pick and choose guns for slots on each section as well as decide whether you want anti-beam coating and armor or not.
This causes MoO ships to be pretty samey, with bigger ships just having bigger health bars and more guns, while in Sots the ships are more specialized on different tasks, like command ships, repair and recovery craft, fuel ships, planetary bombardement ships, assault shuttle carriers, drone carriers, regular old battleships, cutting beam carrying ship, miner, propaganda blaster, bio warfare ship that shoots plague missiles at a planet and more.
Also the random events in Sots are better than the ones in MoO, whererandom events are either you finding a pirate treasure or a pirate planet with treasure or slaves.
Sots events on the other hand can havefalling rocks, extra dimensional monsters, forgotten ancient super weapons, judicious asshole UFO that wrecks your fleets, locusts, swarm, slavers, a propaganda blaster that makes your planet revolt, AI driven ship that turns your planet into a machine world and takes over your ships computers and much more.