Trade:
Trading for resources alone seems like a missed opportunity. Would factions not be open to trading, at a price, with people they are at least somewhat friendly with?
It seems if you’re hostile you can steal their tech, if you’re stuck with the ally mission on the other side of the world you can’t negotiate with them for anything of real value. You can recruit specialist units but you cannot get the weapons required for them. At a minimum I’d think at the time of recruiting a unit there should be an option to buy some appropriate weapons, and factions should trade ammo with those their friendly with (even if at a significantly inflated price to just manufacturing it).
Anu Mutations:
The Anu mutations sounded awesome when first unlocking them, but then I see what they are - Anu’s version of class armour. While it has the positive of allowing any troop to use the armour (I think, haven’t tested proficiency with armour at all yet but it appears to give the option) it just seems to be a bit of a missed opportunity to have more bizarre and flavoured mutations. Maybe even introduce a random element to it - you can select the general type and body area, but it’s a mutation, you can’t control the exact outcome. In game terms I guess I’m thinking less as armour, and more as mounted equipment, add ons which would need to be pretty special to take the place of normal equipment.
If we go down this line of thinking, you could have options for New Jericho around cybernetic enhancements for your soldiers.
Synedrion I don’t know, but given the infiltrators gear there’s still a theme that could be extended.
Either way it feels like there are opportunities here to make it more fun and more troops to be more customized.
I dont want to have stone legs for my sniper 
but random look or additional perks would be great.