From what i’ve seen, it’s pretty hard to avoid the “pervious” posts on the Dope.
I’ve had an idea how to solve a few of the 3-ship problems; how about starting off with a single ship along the lines of the Prometheus, with it’s Multi-Vector Attack Mode (or whatever it was called). In the first…episode? It could split to fight off a foe, and be damaged to such a degree that it can’t reform? Going back to Starfleet and repairing is not an option, since they’re already on the other side of the wormhole, and besides, they don’t have the resources to fix this one ship that can, just about, stay disconnected for a long period of time, when there are other problems that need their attention.
Straight away this would give you “focused” ships; a bridge section (which has…well, the bridge, and most crew quarters and amenities), the engine section (engineering, obviously, and possibly the main computers; i’m not sure how the ships are set out) and a third section (pretty much just weapons on a maneuvarable craft, fulfils the Defiant role).
You’d also be able to get a lot of plot from the fact that the ship/s need a lot of repairs to continue to operate seperately, and also you’d have the Captain be forced to appoint sub-captains from his staff to command the other sections. Plus you could always have a point where the ships ARE able to re-form and the crews are finding it difficult to re-integrate under a different regime.