Ambassador, Oberth, Excelsior, and Nebula all seem to be quite popular ideas.
Definitely. Considering the Ambassador already has two canon variants, the Excelsior has two variants plus a kitbash as another class ( Curry) & the Nebula has around four variants, they would already come to the game ripe for customization.
I also want either the add-on pods to turn a Miranda into Sisko's Saratoga or all the extra canons to make a Soyuz class.
Also, I would love to see Picard's old Constellation Class in with the Heavy Cruisers or the Vesta Class from Pocket Books to go with the Titan.
& since we got the Wolf 359 inspired Cheyenne class, I would love to see her sister ships the Niagara, New Orleans, Springfield & Challenger classes.
In these threads concerning ships that were left out there seem to be a lot of complaints about the constitution class ships being in the game when they're relics, but that's the class of the original enterprise. With how classic that is, and also with the new movie out, of course they were going to include that in the game. They have a star trek game like this where fans of the shows get to take command of a ship, they were not going to leave out the starship class of the original enterprise. They knew there are probably a bunch of people who because of their attachment to that show or the franchise's beginning would love nothing more than to command a constitution class, so they had to have it in there.
As for other ships left out I'm the most surprised I'd say about the excelsior and the nebula since they've both made multiple appearances in the shows. Others listed probably too and I'm just forgetting.
Edit: I was oversaying it with "a lot" of complaints, there are some complaints at least.