Paladin Trooper: I'll bring up what Creator is bound to say: What's the difference between him and Colonel Burton? He can shoot choppers, sure, but that isn't a significant difference. Basically it'd be like allowing you to build 2 heroes. That isn't so much a balance issue as it's a "what's the point?" issue. Why go through the trouble of a new building, new unit and new behaviors to end up with basically what we already have?
Genji: Same idea as above, except you gave a weaker version of Jarmen Kell to China. I can't recall if infantry general has snipers in contra or not, but again, not too much different than what already exists so why add it?
Rebel: I could get behind this, if it didn't sound like the Death Machine from Iron Man 2 (the bigger issue is that he's being recommended for GLA). However, GLA have plenty of anti-infantry firepower, especially with toxins and jarmen kell, and should already be capable against aircraft.
Mercenary: On one hand, sounds powerful because he can kill just about anything. But, he's very fragile for it. I can't imagine him being used much if only because he would be good at base sabotage, but doesn't have the near necessity of stealth.
The issue with the above is you are paying so much in resources for more anti-infantry firepower that most people don't need.
The specialized faction units were just suggestions, but the purpose of the structure is to buff up the infantry prior to Rank 3 to give whoever controls the barracks a tactical advantage against the enemy. I know China Infantry has snipers and that USA has Burton to plant charges, but they aren't accessible until Rank 5 and Rank 3 respectively in 007.
Really the point I was trying to make is that a neutral barracks or Battle Lab (already in the game [inactive and used primarily for script triggers]) should be able to be captured that gives a player a tactical advantage by giving access to a versatile infantry unit that can either sabotage or combat all enemy unit types at a hefty price for infantry.