I am finishing "Goddess of the Moon" soon.. just have been very busy at work. I have only a couple chapters left. Working on an outline for the rest of the story now.
Admittedly, I haven't watched much of My Little Pony since Season 7 - but have seen some episodes of Season 8. So my idea may not fit into much of the recent events- but consider things to be somewhere between Season 7 and 8 - if that helps. I also haven't seen the My Little Pony movie. But I'm assuming that has a lot of one-time celebrities who we will never see again in the series.
A'ight, so this is top third and bottom sixth of MLP episodes. I decided to skew this list more to the top because there are a lot more good episodes than bad ones out there. Also I'd put the pilot episode, Friendship is Magic, at #41/#42. Fairly solid introduction to the series. So these top 40 are those which are better than the pilot.
I'm probably not going to turn this into a story (especially since I have a ton of spoilers anyway), but here's an outline for what I would consider to be an acceptable BB/MLP crossover.
It takes place in some point in Season 4 and is obviously an alternative universe story on the "Breaking Bad" side.