The actual fleet on fleet combat is decided within minutes however the games themselves DO last for hours, and just because you manage to wipe out a huge fleet sent at you does not necessarily mean you have victory in your grasp.
Then again if you want a long battle send flak against flak, that will take quite some time to determine
1 on 1 it actually does takes minutes for anything to destroy its mirror match. For most RTS games that is at most 20 seconds, so by RTS standards the battles do take a long time. If its two large fleets with good defensive support ships it could easily take minutes. And if its a planet siege with starbases, repair bays and titans going at it, that's longer still. If both sides are constantly producing reinforcements it could theoretically last forever, I know I had at least one siege last a half hour, perhaps it was an hour. If the sides aren't evenly matched then naturally it will be much shorter.
It says there are 3 factions but are there more of than that you can place on the map when in skirmish mode?
There are three main races, but each is divided into two sub faction. They specialize in different areas, have some unique abilities and research, and have totally different titan ships. So there is technically six different factions you can assign players too, plus random.