Getting to get my custom Cruiser back at Fleet Admiral would be great, as well as keeping the Galaxy one of my alts is working towards, plus this way guys who get the T5 Excel and GalaxyX are less likely to get screwed.
For T6 I'd like to see customizable looks based on ship class. For example, if the T6 ship you want is a cruiser, then you can pick the parts from all cruisers, Galaxy nacelles, Stargazer pylons, Sovereign Saucer, etc. It would get some additional hull stats.
For T7 I'd like to see customizable looks based on all ship classes. you choose a class to base your stats on but then are able to pick pieces from all available ships regardless of class. Akira nacelles on a Excelsior hull with a intrepid saucer. Once again the hull stats would improve.
I think at T-6 captains should be able to fly whatever ship they want. This is an MMO, and cryptic prides themselves of customization. What better way to customize than to allow whatever ship a captain wants to fly be a T-6.