In ...but Hate the Traitor
, I instantly blew the transport up after I've got the order. Considering the fact that I am totally alone, undercover, knowing nothing about my "fellow pilots" plans, I am helpless to reach Command and I cannot warp out, I was sure that I have to keep my cover and keep on going with the NTF as long as I can. After I killed the transport, they have obviously turned on me but I managed to survive. Guess my surprise when I was sentenced to court martial at the end of the mission.
I mean, I was supposed to say "**** you NTF bastards", then single-handedly kill 5 enemy fighters (which is only simple in FreeSpace context), then... err... wait?! Wait until Command finds me somehow and picks me up, hoping that they don't shoot me down on the way? How could I even identify myself after Snipes was gone?!
I have always considered that mission illogical (and yes, this happened in retail).
As for the original topic, I think that it is an integral part to the FreeSpace story arc that our opponents are 'different' than us. The Shivans carry the mystery, the hidden agenda, the danger, the unknown, and most importantly, an adversary whose methods and motives are totally unknown to us. As for the Vasudans, don't forget that the whole war started based on our cultural differences and that was what made our cooperation ultimately that important and - for me at least - that interesting.
All in all, the original FreeSpace story, for what it is, purposefully makes you the "nameless cog in the great machine" (which is a feeling I really miss and I think none of the mods even attempted to catch this at all, StL had a shred of it but that was satisfying for entirely different reason - as for my mod, I try to keep the player as "nameless coggy" as possible since I consider it to be an integral part for FS) and as such the "humane" part of Alpha 1 is basically unimportant. Of course, they could have written a story with multiple human factions, but that would have been something entirely different. For what
made, aliens were needed. And if you would have wanted different effects, you would have needed a different story as well. At least, in my opinion.