I've been thinking about this as well, since we know level cap will be raised eventually.
Canon-wise, as far as I know, there's not really any more advanced starships than we already have. Cryptic is well within their ability to create new ships for the game, but I've also wondered what'll happen to all the Tier 5 ships we've bought with the C-Store and such. Will they suddenly be obsolete?
It occurred to me that it would be a perfect opportunity for Cryptic to implement an upgrade system for our ships. So we could add extra hull, shield generators, consoles, etc to up the tier of the ship we fly. People have been clamoring for this for a long time.
I have a similar concern. I really enjoy my Tier 5 Ships that I purchased in the C-Store. I would be totally bummed and extremely upset if they became obsolete with the implementation of the Tier 6 Ships. I think that the answer will have to be something similar your proposed upgrade system, or the ability to add Lower Tiered Ships as pets when you become a Fleet Admiral. However, I can see some balancing problems with this. Anyway, I'll pose this question in the next Ask Cryptic.
I like this idea, it would more of a variety at VA, I'd expect to see those missions at 2500 to 7500 exploration badges at relevent levels (or exploration badges significantly reduced from 75 per mission complete to keep the 500 setting).
Possably tilted in favor of upgrades for your class (i.e. science BO abilty/bridge slots cheaper and more available for sci captains). Maybe Cmdr , LtCmdr for relevent class, and one LtCmdr rest Cmdr for cross class (brige officer tray lenght allowing on hotkey 1 or 2 bars).
If Incremental refit options are not viable don't forget that they have only retrofitted up to ships at non token Commander and Captain, all of the RA token ships have still to recieve the retrofit attention.
Considering the Mark/Emblem purchaces other games like WoW already 'discard' much of their hard grinded gear when a raised level cap expansion is released. The only difference is that the C-Store lets you skip that grind. T6 C-Store purchases at cost of 2400 would keep expenditure in perspecive.