It's totally Epona!
No, but really, I personally don't think its Bowser. I mean, if the other dons were getting knocked off, I'd be in hiding as well, Maybe he did take peach for old times sake but Luigi did say he had lost interest in her, and as far as we know, she isn't dead, so I really doubt the "butcher" has her. Another possibility is that Zelda took her to gain power over the kingdom.
I don't think Wario is involved, He seems to do the things he does sort of like Samus but not nearly as graceful, he's just trying to make ends meet and stay in the good books with the remaining people who have "power".
To the person who mentioned the hannibal copy cat, in the original movie they went to hannibal for help with "buffalo bill", a person who was based on a real serial killer, and would lure in his victims pretending to be injured; ie: he would have a sling on his arm and trying to get something large and awkward into the back of his van, then once the victim got into the van to pick up said item, he would climb in and knock person unconscious, go from there. Anyways totally irrelevant but, that was what silence of the lambs was about, the tattood guy was from film "red dragon" which was supposed to take place before silence of the lambs time line wise, but had come out years after silence of the lambs.
Anyways, I do agree I could see the poketrainer being the killer and using pokemon to aid him in the butchering but at the same time, at least in my opinion, that would be too obvious because he IS the "nice innocent guy".
Just my opinions!
