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.