For the score calculations, we don't really publish those too prominently because otherwise people tend to fixate on that, if you know what I mean. But, in general it rewards all the various easily-trackable good behaviors: having a good Kill To Loss ratio, winning quicker rather than slower, building lots of ships, killing lots of ships, having a worse handicap than the AI (or no handicap), not using cheats, winning the game, using difficult minor factions (minor point there), not using minor factions that help you (minor point there), and so on.
Generally, the rule of thumb is: the more efficiently you win, the better your score. If you play a 60 hour game because instead of fighting efficiently you just hit +10 speed to wait for your ships to rebuild after every battle, it won't be as good of a score if you play a 20 hour game where you were fighting tooth and nail every second of the time, and you won after a long hard victory. Similarly, if you play a 60 hour game where it takes that long because you're having lots of detailed tactics and really conserving ships, and your KTD ratio is very high because if it, that will probably be an even better score, etc.
It's hard to say what a "good" score is, it's all relative, right? So it's more a matter of comparing your various games against your other ones, or if you're on Steam you can look at the global scoreboards versus you there. Actually, there's a link on the steam store page to where you can see the global scoreboards even if you're not on Steam.