Disagree completely, a whole cunk of the people playing are after a somewhat Star Trek experience.
Theres already a whole load of people that hate the federation frankenships as it is, no point in alienating them further by adding a crapload of non-starfleet ships.

But personally, i doubt it will "ever" happen, since CBS/Paramount needs to approve a lot of what goes into the game, and seeing as non-starfleet ships in Starfleet is uncanon, then its not going to happen.