There has been a few Star Trek and MLP crossovers. One I think could work for a fan fiction is in the Original Series. All the way back to Kirk! The Episode is "Who Mourns for Adonais?" Season 2 Episode 2 it aired 22 September 1967.

In that episode, the crew of the Enterprise meets an alien claiming to be Apollo. Turns out his race had met humans long ago and inspired the Greek pantheon and myths.

Now I know what the next question is how does this tie into MLP. Well, the Unicorns, Pegasus, and other life on Equestria do have a strong Greek element. My Idea is that what we now know as Equestria or Equus. Was once a colony of these Aliens. Seeded with life from both their homeworld and Earth. That's why it has many earth plants as well as life not from our world.

It would also explain the accent temples Daring Do visits. Including the Fortress of Talacon with the Rings of Destiny could control the sun.

In the Episode, it is mentioned that Apollo has an extra organ that processed energy. The energy that could be magical energy? He does seem to be able to have many magical-like abilities

This is one Star Trek / MLP link a writer could follow. I, however, am not a skilled enough writer to do it justice.

I thought you'd give a mention to William Shatner as a link, but I was wrong. Still, nice idea.

Yeah, tried to keep it in the universes.