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 already started to ship them in the sequel.
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.