Kits can have secondary powers (Borg Tractor beam)
What if you had weapon kits equipable to different ships with different parts?
A hull Kit titled "Cruiser Hull Plating that becomes available at Cmdr and scales with you. It allows you to increase the hull of a cruiser to cmdr levels and scales as you move up, not quite as good as the lowest HP Cruiser but still much better than the original ship.
This would be an engineering console that fits on the ship. Then maybe a Dual torpedo launcher and a Phaser Beam Area Upgrader which would with the console git you extra "powers" of Beam arrays. As you gain levels their power levels up and you can get more pieces so that you can upgrade, at the most, a Cmdr level ship to the current Max tier (Since captain level ships are already retrofits)
These could all be crafted. And once you hit RA you unlock consoles which you can make to increase the power of lower ships that might not have the same number of weapon slots or such.
Obviously the big downfall would be you can't make them as powerful as another ship at that tier but that's fine if you make them really close to it since then you could freely PvE in the ship you like. PvPers, being Min/Maxers usually, wouldn't take part in this retrofitting system most likely.
At least that would allow to use the ships up through the Tiers, although I don#t think that ships like a Miranda or Centaur should be able to beat a Souvereign or Galaxy.
Reading into Dstahl's comments, it would seem that the plan is a scenario where this would be possible... but that the look will probably upgrade with it so that a Miranda or Centaur that beats a Sovereign doesn't look like a 23rd century ship. (Say, it has modern nacelles and a new hull texture.)