I think it's pretty safe to say that the majority of players are very happy with the Refit / Retrofit ships currently available, but I think it's also safe to say that there are a lot of us who would really like to retrofit some of the other older ships.
Admittedly it takes time to QA new abilities and special functions for the ships; but in the interim it would be nice if we could, once we find a ship that we absolutely love, choose to have it level with us.
I suppose the easiest way would just be to have the ship increase its hull / shield capacity as well as console and BO slots with every rank up, but the fun way would be for us to head back to ESD (or even Utopia Planetia, once its available) and pay EC or Starfleet Merits to a quartermaster to have the ship upclassed or retrofitted to have superior hull / shields, more bridge stations, more consoles, etc. Maybe even toss in a little animation of the ship in one of the spacedocks with the little worker bees zipping around it replacing hull plates, shield arrays and/or deflector arrays. (OK so that would take some doings, but it would still be neato. ^.^)
Then as time permits, additional special retrofits (Akira Carrier Gunships, Olympic class with funny looking saucer seps, Cheyenne with slightly less humorous saucer seps, etc.) could be added to the game as separate vehicles.
In the case of science ships and escorts, retrofitting them up to Fleet escort / DSSV levels would not be out of the question, as they are already lightly armoured and armed. In the case of extremely low tier cruisers like Mirandas or Vespers, they could be upgraded as cruisers up to a point but from that point on, the only viable upgrade would be manoeuvrability and armament; effectively turning it into an escort. (Advanced RCS thrusters, better engines, etc. Obviously this would not be an efficient use of resources, but it would be the star Admiral's prerogative to do what she liked with it. (Since we are playing what amounts to a single player game with thousands of other people also playing the same single player game.)
So it would be unfortunate that the early cruisers could not be upgraded to battleship standards, but there is no reason they could not be turned into an equivalent escort. Manoeuvrable, lightly armoured and heavily armed.
In regards to the Nebula not being battleship material, I disagree. In size and functionality it is very similar to the Galaxy; not only that, it has additional weapons located in the sensor pod (Seen in at least one episode firing torpedoes from both the engineering hull and the pod above the saucer.) I see no reason its hull and shields could not be beefed up to Tier 5 Galaxy standards.