Freelancer was one of those games where the actual experience as provided and what you hoped for don't quite mesh. We don't hate it at all, it wasn't a bad game. It had a lot of really good elements, and the whole freewheeling through the galaxy bit was a lot of fun, as were the random pirate attacks on the trade lanes, etc. Getting new ships was fun, even if new and improved weapons were just a different colored laser.
But combat wasn't quite exciting enough, and capships were pitiful. The story, while overblown and silly in places, was really the driving force that kept interest, and once that was gone there wasn't really any reason to keep playing, even though you wouldn't have been everywhere and there are still new and improved ships to get.
The fundamental problem with the sidequests and factions is that other then groups not firing at you or letting you use their base/getting their ships (and reaching the home planet of one normally hostile group due to a fluke in factional allegiance WAS kind of cool) they didn't do anything different. All the quests were exactly the same, just randomly generated. Each base was thus exactly like any other base, with the exception of the items in it. There were no characters apart from the main quests you could get to know or care about, no special missions, no real incentive to explore the outskirts of space other then just to SEE it. And it would usually be pretty much like the explored regions of space.
The game would have been immensely improved by adding non-random quests from each base. As it is though they feel like grinding in an MMO, which is pretty much exactly what they are.