So my question is really for the sake of all the campaigns (and general balance) would it be ok to vary up what I buy, or do I need to buy each factions mirrors? Like if I buy Command Squad for the Allies, do I need to buy the Command squad for the Axis? Same with the special ops, the walkers, etc.?

What I've been doing is kind of building them differently: The Allies have Recon and Command Squads and more Light Walkers, whereas the Axis have the Special Ops and more Heavy Walkers, and I plan to make the SSU mostly air and some walkers, but with several vanilla infiltry units backed by the various commisars. Should this work out for balance as long as everything is balanced point wise or are there things every faction needs?

You can play a good game with any combination of units. But the important thing is to give both sides the choice to use whatever they would like to. If your opponent is fine with not having a command squad, that's not a problem, but it can be a bit aggravating if you go "Ok, I can use this special squad which allows me to reactivate units and bring back dead walkers. You can't have that." One player having a Command Squad while the other doesn't isn't necessarily an advantage, but your opponent could feel legitimately "duped" when he sees you using all those skills, while he was never given a chance to do the same.

I talked about the Command Squad because it's the unit that does the most "unique" stuff in the game. The other units it's more of a matter of balancing out the attack capabilities of the factions. For example, don't get choppers for yourself if you're not going to give the other side some decent anti-aircraft units, and so forth.

Well the allies may get to do cool stuff with their command squad, but the Axis player gets to play zombies and gorillas and snipers, which are all kinda bad ass

I agree. My point is that both sides don't need equivalent units, as long as both players are fine with the units they're limited to.

You need command squads for each faction. You only need one to have those special abilities. I would go for the NCO command squads and use whatever you can get for the SSU.