Pretty simple, add an ability permanently add a different skin to a starship. Example, I want my Oddy to look like a soveriegn, it's statistic abilities unchanged, only appearance. This function would have to have obvious limitations based on shipe class. Can't make a defiant look like a Galaxy, etc etc.
I would rather have the ability to drydocks certain ships and upgrade them, within reason, myself using a pool of options to customize with. But the aforementioned is the quick fix to make all these wonderful, yet obsolete, starships viable and competitive again.
Every Federation Science Vessel will be obsolete, just like every Federation Cruiser play's second fiddle to the Oddy. I'm not bashing these ships, not at all, I am only trying to stress the importantance of varity and personal taste.
I believe this was proposed a while back as "permanent" holoemitters - not my personal cup of tea, though.
The only additional customizations I'd like to see are those for ship interior features (see link in sig for full proposal) and the ability to upgrade BOff stations on any class of ships (e.g. turn a Intrepid's Lt Tac into a Lt Cmdr Tac).