The ability to flag specific fleets to make them continue to exist even if all ships are removed via merging/scrapping/etc would be a nice addition.
And, while we're looking at the fleet deployment screen, Admin Commands could use a little tweaking. They are very handy, but it's a pain keeping them staffed, since "automate assignment" doesn't put officers into them (which I agree with.) Adding the ability to mark Admins so that they notify in the event log any time that the Admin is uncommanded would allows you to guarantee that the important ones are staffed at all times, while not forcing you to keep commanders for all of them at all times.