I'm not that talented, so I'll give just a few sketches
I'd say a compulsory 3+ A-Wings. So you stay close to the original composition, but there is place to add Y-Wings, X-Wings (and that B-Wing) from later seasons. They are mostly recruits under a charismatic leader (Hera or Sato), so I think some support synergy would be perfect. Some way to allow the optional inclusion of the VCX-100 and shuttles would rock.
Concord Dawn Protectors
A Protectorate Starfighters only squadron. Think on über-pro mandalorian pilots. Maybe some kind of skill sharing target locks. In the series you can see them flying as beasts; maybe keeping unused focus token to exchange them for barrel rolls and boosts later?
Bounty Hunters Guild
That's is quite hard, because the ships available for the squadron would be limited but extensive: G1-A Starfighter, and all the Scum large ships. What about a "1+ large ship; large ships and G1-A only"? I can imagine them collaborating and competing at the same time. Maybe some way of stealing tokens from friendly ships?
Lothal Imperial Research Facillities
Only TIE Fighters, TIE Interceptors, TIE Bombers, TIE Advanced Prototype and TIE Defender. The Inquisitor and Valen Rudor as possible unique pilots. I'd see them as testing pilots so maybe they would look similar to your Black Squadron "neverending TIE Fighter waves". Or something about the TIE Fighers acting as scorts for the TIE Defender and/or the TIE Advanced Prototype.
Man, I just can say I love Star Wars Rebels as much as I love your work
PS: there are several links in my text, check them out!