I had an idea a little while ago about when levels past vice-admiral get put in game, you get the ability to summon ships that look like your previous ones and use them in the same way carrier craft or even Boffs are used.
What would be nice is if you could select a ship from your hangar, essentially save the design in terms of boff abilities and then call it to battle every 10 mins or once a match. It would have all the items you leave on it though so best not leave it with rubbish stuff!!
Apart from being really awesome to call in something like a JHAS or JHHEC when in a JHDC it would serve as a big resource sink for Cryptic as you will no longer be just getting sets for one ship and switching, you'll get them for several.
If the save function is a bit much it could just give you a list of abilities and slots to put them in which will just be spammed when they can.
Imagine, you could call for back up and have a healer set up ship as you customized coming in and heal you, or a tank to generate and keep hate. Could also help people understand the way some abilities can be shared and some cannot and their impact on the team.
This would involve a LOT of work with AI programming (if those ship's equipment would be customized by you). I doubt this will ever happen.
Maybe not as much as you think. The AI code for ship combat has aleady been written (at least to some extent). For example, fleet support, romulan distress calls, hanger pets, Haakona class warbird, multi-vector advance escort, and the occasions when you automatically get a single ship support (like when the Enterprise shows up sometimes during the Tau Dewa Sector Patrol). These are ones I can think of off thr top of my head.
As far as customizing the ship setup, a form of 'save' already goes on when you equip the ship you use. All of your ship's traits are stored in a database anyway, so it wouldn't be too far of a stretch to have two active ship profiles up to date. Then you specify what boff abilities (maybe limit to three or four instead of the normal layout to make it a little more balanced).
Another thought on control would be that the ship in question would be directed like a hanger pet, and it's boff abilities would be triggered automatically.
It'd be a bit of work, but not necessarily as much work as you would think.