The Inquisitor is Discord in disguise.Think about it. Nightmare Moon herself can't remember when he started working for her, and he knows her real name. On top of that, he keeps his entire body completely covered, except his face, which is gray (note that Discord has a pony's head, which is gray in coloration). Perhaps Discord somehow got loose from his imprisonment when Nightmare Moon defeated Celestia and decided to play things safe this time around, subtly brainwashing Nightmare Moon in order to get close enough to her to manipulate things to his amusement.
- Probably Jossed by the latest chapter, which shows the Inquisitor alone in his private chambers, without his suit on. Since he doesn't revert to Discord in this time, it's probably not him.
The Inquisitor an alicorn in disguise.The Inquisitor is much, much older than he looks, and knows Nightmare Moon's real name. He keeps his body completely covered when not alone in his private chambers, except for his head and unicorn horn (while Discord's pony head is gray, he has neither a unicorn horn nor a black mane). He is a skilled magic user—it's rather heavily implied that he's affected NM herself with the same spell he uses on Twilight. All of the clothing in his wardrobe is long enough to cover a cutie mark, which means it's more than long enough to cover folded wings. While no mention is made of wings while The Inquisitor is relaxing alone in his chambers, nothing in the scene would require it unless a reveal was scheduled. When Twilight comes to visit, The Inquisitor goes to get a dressing gown—why would he need to go get dressed unless he's hiding something, since nudity is the norm, even in Canterlot? Given his coloration, he could even be the alicorn NM thinks of occasionally, Storm-something-or-other.
The Inquisitor is a Time LordHe's from a village in Gallopfrey, doesn't seem to age (or does so slowly), and is known by a title instead of a name.
The Inquisitor is Sombra.Obvious in hindsight. He's known Nightmare Moon since she was Luna, he's a grey unicorn stallion and he'd likely have the power to indefinitely prolong his life.
The Inquisitor Is Star-Swirl The BeardedBecause...reasons.