While I agree with you that fighting human enemies has greater depth to it, I can't agree that it does anything to harm Freespace's plot, because the aliens are so integral to the plot. Freespace is based around the idea that an interspecies war caused Terrans and Vasudans to learn how to adapt and survive, and built on the mistakes of another race which came before them, and was wiped out by the Shivans. You couldn't achieve that without having Alien species - The fact the T-V war was interspecies is what differentiates it from all other wars, and you can't substitute humans for races which are several millenia old and keep it in any way similar to the current plot.
In FS2 a human enemy was a realistic prospect, there had been no war for 3 decades when the rebellion began, and there was a solid reason for the NTF to exist, in FS1 with the background of a long interspecies war (central to being able to survive against the Shivans) an intra-species conflict would have been highly out of place - no rebellion in such a situation would gather enough support to survive, because people would be too scared of the other species taking advantage and attacking. The HoL was reasonable because of the religious alien aspect, but it's not plausible for humans to turn against each other in a war of survival.
In Freespace 2 a human it was well done, but asking if the amount of aliens limited FS1's plot is like asking if the plot of Titanic was limited by the fact it's set on a boat.