I know it's been brought up before, but please allow transfer of ships between fleets of the same faction. I want my main fleet to have the newest and best ships, but having to disband my rank 4 cruiser rather than passing it to an empty garrison admiral is very frustrating. Considering ship construction is handled by sector, it's a pain to have to send your admirals back to reinforce at your hub rather than just transfer ships between fleets. Further, funds might be rather tight in the campaign so having to rebuild ships rather than pass them on is frustrating for the player also.
Would be relatively easy to organise rules wise. The two fleets must be in the same system, and no other fleets must be there. Then, clicking on the system could bring up a button next to the 'new fleet' button which would allow the exchange. A window would then come up listing the ships of both fleets. From there you could simply drag and drop between fleets or use arrows to move ships back and forth. A simple display down the bottom would show the fleet capacity of both.
This should cost all remaining movement that turn to represent the time taken to reorganise commands etc.
This is a pretty standard feature in all grand strategy games and it allows you to more efficiently and effectively use the campaign strategically.