Well, I would say don't get your hopes up about Fontana. I'm not saying don't try, because it's always good to dream big, just don't expect it.
It sounds like you're not looking for the traditional ship/crew Trek format, but more of just a basic dramatic/political/adventure story that takes place in the Trek universe, and maybe deals with Spock? That is, do you intend to have a starship bridge crew as the main characters, or somebody more like Jack Ryan in Hunt For Red October? (Or had you not decided yet? That's fine, too.) Most people are used to seeing Starfleeters as the heroes of a Trek story, but it might be interesting to go for something a bit more germane, like (just off the top of my head), Spock and Saavik, with a Romulan confederate, and a couple non-Starfleet humans. Just the same, Starfleet is the heart of the Trek-verse, so we would probably want to have a starship captain, (and his ship/crew) at least as a supporting character, but it would kinda be interesting to do a feature where the captain wasn't the star.
The other thing I should mention is that, like I said, I'm really most familiar with the TOS era, and as far as continuity references and historical-period accuracy for a later era, I'll pretty much be no help. But if someone else can furnish that aspect, I'll certainly be able to help with the more story-based plot elements.
Any of this sound good to you?