Well, just adding a throught about Mutie slaves and upgrading to mutant military units (didn't found a better place to post them):
The Mutie slaves, as I see them, are humans from armies, caravans and such, that where captured by the Unity. After being captured, they where dipped in the vats. The Mutie Slaves, as the unit themselves, are newmutants, so they mutations are develloping.
Think about the slaves the Enclave used in FO2 to find FEV in Mariposa. They're slower on work because they still try to get the hang of a changed body and even a changed mind.
They can upgraded to military units. The way I see it, the mutie slaves, after having they bodies more stable, are selected. These mutants, then, have doctrinary (I think that's the right word), military and mental training to join the unity. After that, they are mutant soldiers, ready to kill and die in the name of the unity dream of equality.
Something like this would be interesting in the civilopedia.
Some other suggestions:
BOS: The way I know the BOS, they're a ellitist organization, so they don't expand much and don't get much recruits. But, the way I see then, they got some pretty good hardware, and will recruit IF needed. So, what about giving to the BOS a "Recruiter" unit as settler. It should use more people, but be EXCELLENT soldiers, and the hability to enslave. Besides, BOS should have pretty good scientists and something SPECIAL that would make better soldiers better than more soldiers, if you know what I mean.
NCR: NCR is ok. Expand fast like cockroaches. Something more about culture anexations for them would be interesting, kinda like NCR-style.
Enclave: What about giving then a Vertibird unit from the start? Not a full-strenght vertibird, of couse, but, what about a prototype? Would add a interesting twist to the game.
Unity: What about the Unity producing Floaters and Centaurs as units? Enclave have the Deathclaws, and that's all right and cool (I like then... on my side, of course), but what about unity with Floaters and Centaurs? The Master's Vault had some of then, the mutant patrols tagged along Centaurs and Floaters. Same thing to the Remants of the Master Army of FO2.
Could add quite a interesting edge to the unity.
Robots: What a Eyebot serves for?
Children of Set: Looks cool, need to play with them.
Vaults - What about some kind of bonus about food, or something related to a G.E.C.K? Bessides, they should get a NICE start, don't they?
General - What about adding a building that each 20 turns spawn a TOTALLY RANDOM unit? I mean, RANDOM! Say... Like something called "Weapon Salvagers" or even "Gun Runners" (I liked that). It would represent the scavenging of weapons and armor after the war, and that building would apear early (but not too early). A Example: You're the Children of Set, and you're fighting NCR. You both are on a stalemate of Milita Troops and some rifle infantry. Then one your gunrunners spawn a Early Power Armor, and other spawns a leather flamethower. Yeah, the ideia is quite weird, but it can add a interesting randomness in the game. What do you think?