Switching from ship to ship doesn't seem very "realistic". Personally I would put all my best weapons on the fleet ships while keeping the best armor/shields for myself. Acting as a command ship on the sidelines.
Given the limited selection of endgame gear it wouldn't take long before the fleet also had good armor/shields and my ship had good weapons.
The programming would be a massive undertaking though, Let's say you have a fleet of yourself and 4 ships (just like an away mission). You choose Exploration cruiser and Exploration refit, each with saucer sep mods and advanced tac with advanced tac refit each with MVAM mods. That give you a fleet of 10 ships plus yourself. When the MVAMs split, which one keeps the weapon loadout and which ones become pets? How do you issue orders, are you controlling all 10 ships or just the 4 "primary" ships and their pets follow them shooting randomly?
I would really love the idea, but I don't see it happening. I'm having fun just imagining it...