It's not about the nature of enemies - alien or human. It's not about how many Terran factions there are. It's not even about whether you can empathize with your foe or not. It's about the quantity, detail, and quality of information about the game universe, and how the plot takes advantage of it.
FreeSpace has plot, but very
little lore. If you compare the amount of lore provided as backing material to FreeSpace with that of Wing Commander, Wing Commander wins by a landslide (it provides massive star maps, historical time lines from the start of the Human-Kilrathi War to the end of it, dates and times, important political characters and their motivations and personalities). Volition barely bothered
Volition skipped the entire Terran-Vasudan War to get straight to the Shivan aspect of things. Vasudans are people too --
could have spent an entire game fleshing out the Terrans and Vasudans, providing backstories, factions, politics, leaders, peoples, their hearts, minds and (very differing) philosophies. After playing that game, the player might object to the alliance with the Vasudans just like other pilots by the time the Shivans showed up - or even empathize with the Vasudans. Volition didn't bother.
Volition focused on a very simple plot - two sworn enemies unite against a common, completely unreasonable foe, vanquish it, think they're awesome, and get humbled by that same common foe later. Unreasonable foes like Shivans do make easy to write plots, but mainly because when the plot is "for humanity's survival," it's easy to dodge the question "Why am I fighting? What am I fighting for?" with the answer "To save mankind," rather than "for moral value X or moral value Y."
"Aliens are attacking, go save Earth" stories are easy to write. You don't necessarily need a whole lot of lore or backstory for this to be exciting, and it's difficult to cram lore into a mission based format without having too much exposition. The fact that Wing Commander bothered to provide the informational lore that it did (via game manuals, tech databases, cutscenes, etc.) is admirable; it went above and beyond the call of duty required to keep a player mindlessly fighting towards the next mission. It gave them a universe.
It was Volition's choice to make their universe so simplistic. Don't blame the Shivans - blame Volition. Volition still could have provided information about the Terrans during the war against the Shivans which would have made the player wonder who they are fighting for. They sort of touched upon this in FreeSpace 2, but never got much further than a single pilot complaining about the Iceni.
I do believe that the Terrans could have been explored a little more. Some of the biggest depth we got was knowing that corporations still exist in the GTA / GTVA, the GTI Rebellion, and the motivations of Admiral Aken Bosch and the NTF. I spent a lot of time poring over the Tech Database's descriptions of Earth and Humans, wanting far more than it gave. What about how planets are governed? What are the people's rights? Are people happy in the GTVA? What about civilians?
The lack of information like this tends to force us to make up our own. And that's what we do with our user-made campaigns...