This is one of those topics that has appeared somewhere in these forums since before the game launched last year. I'm thinking the months following the games second-year anniversary (February 2nd) may inspire similar observations from a fresh crop of F2P player's.
Some of us have been clamoring for the privilege to at least upgrade within ship types. For example, keeping the skin of your favorite lower tier Science ship. Or, say, from your Lt. Commander Escort configuration to Commander Escort configuration as you rank up with the choice of keeping the skin you have or to buy the new one. Which doesn't affect balance at all.
It seems that the strongest player objection being from PvPers. Who, under the current system, wish to avoid confusion from the wrong visual cue (being the starship skin). Though I've always felt STO needs a better method of using sensors to determine the actual nature of both the PvE and PvP opposition. I would think player's in a Star Trek game would expect this to already be the case. Such a game mechanic might be more sophisticated, but Star Trek is supposed to be (more sophisticated). This is some depth that can be added into STO. The question is will the Dev team deem it worthy of the things-to-do list?