I agree completely Sig, about the Emissary. Otherwise, it would be much better to transport a diplomat on a Protector, or even a Courier, if the goal is to GTFO more rapidly.
Nate:
It is a big deal. If you don't want to change the status of the Custodian's movement, you will be ruining the whole flow of the fleet. Your fluff examples are personal opinion, and as it is you have a flagship that stumbles about while the rest of the fleet is forced to stay with it if it wants mutual support. Thats broken to me. Oh and deflector shields, willing to take a price increase for that.
The community as a whole wants this Nate, please give us a better reason if it just cant be.
Otherwise, its just personal feeling. Except the Emissary, the main variant should have 2 fighters, to be balanced with the other variants. It doesnt make sense for the torp options to be more desirable than what is obviously the main build. 25cm makes sense on it too.
Great job on a great fleet.