If the cryptic have some difficulty ( as seen by the complete lack of original missions ) A fantastic way to get canon type missions would be to recruit one or more of the series writers. They already know the layout of the ST universe and had litteraly hundreds of show ideas.
I would also suggest getting some voice overs for mission screens, doesnt necessarily have to be a star at least someone with some skills. Not only would it make the missions more interesting but it adds a level of detail sorely missing from the game.
Get the deep space genesis engine working, ST is all about EXPLORATION, the explore missions currently in game are dismal at best.
I have seen far too many negative reviews for the game to date, especially Gamestop, they are really dissing cryptic you might want to have an attourney remind them about defimation of character.