It's not a development I'm overly keen on, but from a story-telling perspective, it would certainly be a fertile ground.
I, for one, was extremely impressed by the latest Intrepid episode and wouldn't see any reason for them to change direction because of a shift in the industry. I also think it remains to be seen that the "relaunch" of Star Trek will be a success, in the long run. The movie is extraordinarily popular, but the plot device used to propel the story is pretty stale in science fiction. What will really be the test is to give the characters and the new feel an actual, you know, story to act out.
What sort of confuses me about the new movie and this new approach is that... outer space is pretty fertile ground by default. What's been killing Star Trek (at least conceptually) for years is this shrinking of the galaxy, this portrayal of space as a place without danger and without wonder. And without diversity. I think Voyager and Enterprise tried to break out of this, but they didn't do it very well.
If Star Trek lacks fertile ground, it's because the earth's been salted. I don't think that recent episodes and movies really tried to be bold, and I don't think they resisted the urge to fall into comfortable plot lines and questions that have been answered over and over again. The best fan films are the ones that arose not to continue the saga (so much as I've enjoyed Exeter and Phase 2) but the ones that were started to answer new questions about people (Hidden Frontier) and space (Intrepid). So long as Intrepid is asking questions about what it means to be human in the vastness of space, in a place that people don't really understand, it won't need to worry about fertile ground, as its roots are firmly planted in it.
(I would, however, back away from the Section 31 stuff, as it's being used by just about every fan film and is pretty tired, in my opinion. But that's juts me.)
