WMG / The Equestrian Wind Mage

Dethl is Vaati's father.

For an utterly evil demonic being who likes Mind Raping others with nightmares, Dethl seems awfully concerned with bringing Vaati back into the fold, as opposed to Majora, who wants him to suffer. Add to that the fact that Vaati is part demon, and never knew his parents, and it starts painting a pretty clear picture.

• Further evidence — Dethl is said to resemble Vaati's demon form.
• Not confirmed yet, but strongly implied by Iemanis' comments during the Battle of the Everfree. Luna, at least, seems to suspect this.
• Confirmed by the official Universe Chronology.

Ghirahim will stab Majora in the back in favor of King Sombra allowing him to become the actual Final Boss.

Ghirahim is Demise's servant, and Sombra's stated to be an alternate Ganon. In Hyrule Warriors Ghirahim sides with Ganondorf for being the incarnation of Demise's hatred. Between an incarnation of his true master and Majora, Ghirahim chooses his true master.

• Except that calling Sombra an "Equestrian Ganondorf" has just been a metaphor on Vaati's part. They're not the same individual, as shown by the fact that Sombra has been resurrected and is running the Equestrian Church of Majora while Ganon is off fighting the Mane Six. They're not the same person.

It'll be revealed Vaati's Big Bad stomping did more harm than good.

The excuse for Ganondorf being able to overpower the Elements was that Ganondorf had more stamina. Thanks to Vaati, the mane six were never tried by Discord, which naturally would've made their friendship stronger NOR had to use the Elements a second time, and weren't as heavily taxed by Chrysalis either. In other words, the Elements might have been able to beat Ganondorf without Vaati taking out villains for the Mane Six. It'd be a nice Deconstruction of Vaati's status as a Possession Sue.

• I, the author, hereby admit that this is a very interesting way to think about it.

When she's fought, Starlight Glimmer will be referred to as a "cheap Grey Hoof knockoff".

Because let's face facts, that's just what she is — insane cult leader of a small town, convinced Cutie Marks are inherently evil, unwilling to admit when they're wrong and, in the case of this 'verse, blindingly willing to sell out to a villain who is just using them to further their own goals. Really, how could Vaati refuse to lampshade that? Or Applebloom, given her history with the Blanks?

Tirek will eventually stab the rest of the Villain Team-Up in the back.

Tirek isn't exactly known for being trustworthy, nor has someone being stronger than he is stopped him from screwing them over in canon. That and at full power, Tirek is leagues stronger than Sombra, who is supposedly comparable to Ganon, so at his full power Tirek would likely be a major threat.

The Church of Majora will ultimately be its own worst enemy

Okay, we've got two power hungry people willing to go to any lengths to get the power they want, one insane Knight Templar, Grogar, several demons (one of which has Undying Loyalty towards someone who he's being kept in the dark about having been resurrected and then permanently killed), several monsters, and King Sombra, who's stated to be comparable to Ganon.

They're working together fine now, but sooner or later, possibly even INTENTIONALLY on the heroes' part, all those conflicting traits are going to clash and infighting is going to happen.

• Majora, being the God of Evil and all, likely knows this is a possibility, and will probably make sure they keep working together efficiently under threat of retribution if necessary. Of course, after he successfully takes over Equestria, he'll no longer need them, and could very well let them all rip each other apart...