Charles Atlas Superpower: To compensate for his lack of magical ability, the Grand Ruler trains him intensively to be physically stronger and faster than the other characters. Somehow, he still finds himself tuckered out by carrying crates and baskets of vegetables.
Royals Who Actually Do Something: Invoked and Averted. While he takes constant care of the ecosystem of Unicornicopia, he does not go into battle when Titan shows up the first time, despite being the only one able to stop him. The author later tried to excuse this by explaining that the Grand Ruler had faith in his prized student, Lightning. Problem is, Lightning can't use magic and the only reason he did not die is that he conveniently discovered he can summon the Uniforce.
Disproportionate Retribution: He got his face disfigured in his past and got shunned by everyone for his hideous looks afterwards. Years later, he kills his entire species and starts to destroy parts of the multiverse for no other reason, than that it is fun.
Generic Doomsday Villain: He has all power and wants to destroy Unicornicopia just so he can spread chaos and destruction over reality, just because. His dialogue is dripping in clichés and there is nothing unique about his appearance at all. Being Stupid Evil and going with the first Saturday morning cartoon plot his minions come up with doesn't help matters.
invokedPalette Swap: She is according to recent videos just a Rarity clone, but not as shallow as the original. He has tried to cover this up by... slightly darkening her coat, which he feels "ruins the design".
Satellite Love Interest: We never learn much about her other than her interest in astronomy, which is practically forgotten after her introduction. She doesn't even appear in the author's video of character bios for the fic!
Demoted to Extra: He was a core member of the team in the initial series, was removed for several stories and when reintroduced in My Brave Pony: Star Fleet Magic III, was a minor character. The Deviant ART remake brings him back, not as a member, but as a recurring background character.
What Measure Is a Non-Pony?: They are artificial beings and considered not worth rescuing by the heroes when the reality they fought in starts to collapse around them and they are too weak to escape.
Why Don't You Just Shoot Him?: In one chapter, Rep-Stallion is ready to deliver the killing blow towards Lightning, when Titan calls him back for no reason at all. If he had just given him five more seconds, the hero would have been dead. Titan later explains that this is because he wants Lightning alive so he can take his powers. Not exactly the smartest plan when Lightning is the only one who is able to defeat him and he's conquered worlds without the Uniforce before.
Chickification: In canon, she's a competent and wise ruler. In here, she clings to the Distress Ball with a firm grip and runs with it.
Villain Decay: Reduced to a brainwashed monster henchman of Big Bad Titan near the end of the story and loses his reality warping abilities. To add insult to injury, he gets killed by Celestia.
Remember the New Guy: He is Krysta's adopted son, who suddenly appears with no foreshadowing in My Brave Pony: Star Fleet Magic II, Episode 1. When asked about why he suddenly appears, Mykan answered "New characters get thrown in all the time (everyone knows that)".
The Complainer Is Always Wrong: He falls into this, as well as Strawman Has a Point. He gets kicked off the Wonderbolts for complaining about Starfleet, and is portrayed as a loser who lounges around the house all day - even his own sister disagrees with him and has little sympathy. He ultimately ends up getting arrested after threatening to kill his sister in a fit of rage, and is Brainwashed to like Starfleet. However, he comes off as more accurate than the author intended regarding Starfleet's flaws and failures.
Flanderization: In his first appearance, he does hate Starfleet, but has other priorities such as his sister. By the time of My Brave Pony: Star Fleet Magic III, all he does is rant about his hatred of Starfleet and hates his sister.
I'll Kill You!: Says this to Skye after she declares him to be as bad as the evil they face, which results in him being officially declared a criminal, beaten and arrested.
Why Don't You Just Shoot Him?: Happens in My Brave Pony: Star Fleet Magic III, Episode 11, where she is called away by Sombra when she is about to kill Royce and Pinkie Pie, though at least there's a reasonable explanation (She already got the Crystal Heart Sombra told her to get).
Blood Knight: Actually betrays Sombra over his feud with Lightning Dawn.
Make Wrong What Once Went Right: The Dark King has conquered most of United Equestria in the future, but faces resistance that prevents him from finishing the job. Thus, he goes back in time to try and prevent Starfleet from winning in the past