Currently the FIA are marked as Independent in Zeus, which makes no sense as they're meant to be allied with NATO in the canon.
This makes it impossible to include FIA, NATO, and the AAF in a canonical mission, as both the AAF and FIA have to have the same status with NATO. The AAF and FIA are specifically meant to be opposed to each other, and yet they're technically under the same faction. Having them locked in to BluFor (as they are in mission editor) seems also limiting.
My personal recommendation would be to create a 4th faction, GreenFor, for the AAF, whilst keeping the FIA as "independent" as they truly are an independent small group. This would make it possible for all possible combinations (and canonical combinations which cannot currently be done) to be achieved.
e.g. You can have AAF + NATO pre-war, you can have AAF + CSAT vs NATO + FIA, you can have FIA vs AAF, etc.