do I get this right that on a T5 escort you get 2 science Officers but have to discard one when you get to T6?
"Sorry, Spock, gotta go. Scotty is taking your place"
No, that's the same Tier of ship. At Tier 5, you get to pick a ship that is either more tactical or versatile. A straight up and down slugger or something that could choose to be more of a tank or support ship.
Long term it would be nice if they added stats for each section. Picking a 'pure' class (all the same pieces) would have its own 'item set' bonus, but you could mix and match hull, saucer, pylons and nacelles for various strengths/weaknesses.
Then what would also add to longevity would making those pieces further open to customizing. Maybe make them slotted and you can apply various 'gem' mods to them to further buff them. With the appropriate star trek technobabble, of course.
I think it would help if there were some differance between the ships in the class at the different rank. For example look at the cruser class rank 2. you have the constitution refit, excaliber and vesper class. If each had slightly different stats it would encourage different play on the ships. say the constitution class had a slightly better power supply, the excaliber had slightly better hull rating, and the vesper had the ability to carry an extra device it might cause folks to pick different ships based on it. Don't make the differances massive. The extra device might be too much, but if there are "historic" differanced between the ships let them play in. There is no fleet in the world that puts out 3 classes of ship with the exact same capibilities.