You can kinda sorta say that Donatra is in-game. She's in one of the STFs. If I recall correctly, she teamed up with Picard in Nemesis to stop Shinzon. A nice Romulan, imho.
The reason we don't see many of the characters in the game is because Cryptic needs to pay them in order to use their likeness. They also need to get permission from CBS.
Where Worf is concerned, I think he aged to a point where he doesn't look like Michael Dorn anymore and therefore they can freely use that character. This is also the reason why you see a lot of the children from the shows (such as O'Brien's son).
The story of the Enterprise E for this game says something about them being away on some deep space exploration mission. I'm guessing the purpose of the F is to have a new flagship while the E is away on its mission.
They are probably never going to say anything about the E because of CBS. I'm assuming CBS doesn't want STO to touch the E because in the future CBS can continue the story with it.