Implications? The author himself said that "she makes him see sparkles before her eyes" and that he has a "harmless" crush on her. By harmless crush, I mean he had her get married to and have children with his Self Insert.
Although you need to be a little bit of a bastard to find it funny, the author himself. Just how deluded can he get?
Provided it isn't actually some brony being a Troll to everyone, that is.
The sad thing? He's really, really not kidding. A look through his ff.net archive has him doing this sort of thing since 2006.
Pretty much any MST or other mock of this author's work. Seriously, with such low standards, it's hard to fail at making it funnier or at least more tolerable than the original source by itself. With the "Starfleet" stories, it's like the author made the My Little Pony: Friendship Is Magic fanfic equivalent of Sonichu.
During the confrontation with Ace Ray in Part III, someone finally gets fed up with Rhymey's rhyming.
Rhymey: There's no need to make a fuss / there is nothing he can do to us.
Ace Ray: And you... will YOU STOP WITH THAT RHYMING!
Given Mykan's tendencies to steal material, referring to Starfleet as "original space ponies" in the first episode of Season 2.
The fact that the protagonists are seriously frightened (though partially due to a curse) by bad dreams in one chapter, to the point that they're afraid to have anything do with their hobbies for several hours. Contrast that with the Mane 6's reactions in the FiM episode Do Princesses Dream of Magic Sheep?, where they were scared for only a few seconds when they woke up. Curse or no curse, it makes them look incredibly incompetent.
Though it was revealed to be a troll, the idea of an African preacher plagiarizing Mykan's work. The irony is delicious.
This little gem from one of the earlier chapters, which manages to be genuinely amusing:
Lightning: Although a blood-curdling scream is just as good.
Some of Mykan's Rouge Angles of Satin moments are pretty hilarious, but one in particular stands out. Early on, resident Generic Doomsday Villain Lord Titan has the "heroes" right where he wants them, and gets thwarted by the timely arrival of Dyno and Mite. When Lightning gets free, he shoots Titan a look of furry.note It's supposed to be a look of fury, but then again the MST wouldn't have anything to make fun of if it were correctly spelled. Or written. Or overall competent, for that matter.