Ok, so literally I just had this idea. The concept for having these non-Starfleet faction starships to be so rare is because CBS didn't want a game about The Federation to have every Tom and Jane flying in Jem'Hadar, Ferengi and Cardassian cruisers. So make them super ultra rare, and have only a small number of them in game.
SO, my idea is do the same thing. But instead of having a special ship, we get an "upgrade token". This token can be used once, on any Starship we have in our inventory. It will boost it up 1 tier. People will pay BIG BUCKS to get their T5 Akira's, Connie's, NX's or Type-F shuttles (I don't judge).
Crazy idea, I know. But if the name of the game is revenue for Cryptic. This is definitely one thing they should consider. People get their ships they want, and Cryptic get $$$$$$$$$$$$$$$$$$$$$ in the bank for it. AND it prevents the game from getting full of T5 ships that shouldn't exist... Per se'.
I know I'd pay for as many boxes as it took to get a T5 NX.