The idea is good and has been discussed on the STO Forums before.
If don't think it would be THAT easy to implement because they would have to make up to 5 different versions of each class. One less for each following tier.
With the exception of the starter ships and a handful of others (Constituition, Galaxy-X) you can, however, get a very powerful refit or even more powerful fleet refit version of nearly every ship in the game through the Starbase system.
For that you need to be in a fleet that has some provisions for a ship purchase available and you have to have fleet credits and fleet ship modules available.
Depending on the tier of the starbase's shipyard you have access to different ships.
The TrekBBS Armada has so far unlocked 3 ship yard tiers, which makes almost all of the lower tier leveling ships available.
A refit ship costs 1 fleet ship provision and 200,000 fleet credits (which you get by donating resources to the fleet holding projects).
A fleet refit ship costs 1 provision, 20,000 fleet credits and 4 fleet ship modules.
If you already own a c-store version of the ship, you get a discount on the modules and only have to pay 1.
The modules are available via C-Store or from the exchange.