Even if we are talking holograms of those ships we love so much, still for the game itself I still have to say no, i would be completely against it, simply due to the two facts
Wolf in sheep's clothing
complete overhaul in space combat mechanic.
The wolf in sheep’s clothing argument only works for PVP because in PVE it is really meaningless. How is it a wolf in sheep’s clothing if the wolf must remove the sheep costume before going into PVP? Did they totally overhaul space combat system mechanics to add the ship holo-emitters that are currently in game? It does not affect your game, but it could make the experience better for other players. It does not unbalance the game, require the changing of combat mechanics, and it simply expands on something that is already in game.
How horribly troubled were you that time I used a Jem'Hadar holo-emitter on my Defiant? How bothered would you be if I was about to make my Defiant look like a Saber in some random no name instance? I am not that crazy about ship appearance tabs or holo-emitters. I just see them as a PVE oriented compromise for players that would like to use a low tier ship with high tier ship abilities. It is much simpler than redoing the tier system or retrofitting ships and does not affect PVP.
This is not a serious Star Trek game, so do not pretend that it is. Adding more ship appearance options is not a slippery slope at this point, but it is just making an already vertical surface taller.
I do not have a problem with excluding the TOS Constitution or if they must exclude the other T1 ships because of a request by CBS. However, I have heard no such thing about the other low tier ships like the Saber, Akira, Nova, Olympic, and Cheyenne. This also does not including whatever future low tier ships they add. They cannot make everyone happy all of the time, but with an appearance option or holo-emitter for low tier ships they could make some of the people happy some of the time.
Another thought is to mix the ******** player community notion of gear score with City of Heroes' arena system (where you use pets) with the pet system in STO which will eventually include ships.
So... A level 10 mission would have a "budget" of 1000 points and a Level 50 mission would have a budget of 5000 points. A Connie would be worth 1000 points. A shuttle might be worth 500. A Galaxy, non-refit, might be worth 4000 points. A Nova would be worth 2000 points.
So.... You do a level 10 mission, you have to swap down to a Connie or a shuttle and one shuttle as a pet.
You do a level 50 mission and you could use 1 Galaxy and 1 Connie, 10 shuttles (9 of which are pets), 1 Sovereign, 2 Novas and 1 Connie, etc.
This way, you would design it so that mission XP scales but content doesn't and you'd use have to use lower tier ships for lower tier mission replay.
I think this way would be the best but would require some rethinking of Remastered episodes and Feature episodes being level scaling. You scale to the mission based on what you're allowed to bring. The mission doesn't scale to you.
I'm still pretty hostile toward the idea of commanding a fleet. That's not Star Trek at all to me. One ship, one crew are the norm - fleet actions are the exceptions.
Tiers are gone. Instead you have generations, you start the game with a generation 0 ship, your training vessel whatever. After the tutorial you then get assigned your first actual ship, generation 1.
Generation here means developement progress, nx-1 is a gen 0 ship, conny would be 1, refit conny2, ambssador 3, gal 4, sovy 5 for example.
So now you are in command of your ship and rank up, you get the choice of switching to a newer ship design, higher generation, or upgrade your current ship with newer tech, raise its generation. Each generation raise costs more and more. merits, crafting materials etc. This should balance out gen1 ships overflowing end level games, unless the player really wants that ship and nothing else. like +1gen costs normal, +2 costs 2x, +3 4time, +4 costs8 times as much.