I've been watching There Will Be Brawl. Think Smash Bros. meets Sin City. I've gotten more motivated to try to figure out who the butcher is before they reveal it since the creators are claiming it's a fair play mystery, and we should be able to guess based on the clues so far (and, I presume, knowledge of the characters from the games). Also said it won't be someone "out of left field." Some evidence and thoughts of mine (and possible spoilers for those who haven't watched, yet) are below the fold.
Leaves behind the internal organs, minus bones and skin. Included some flair with Mewtwo's remains popping out of a pokeball.
Able to sneak into and out of DeDeDe's room and perform the total disembowelment without getting caught.
According to Link, some skull fragments in his remains indicate he was struck from behind with blunt force.
Victims so far:
Pichu (Pokemon, Meta-reason: Removed between Melee and Brawl)
Roy (Fire Emblem, Meta-reason: Removed character)
Mewtwo (Pokemon, Meta-reason: Removed character)
Princess Peach (Mario Franchise: Kidnapped, death not confirmed)
DeDeDe (Kirby Franchise: First killing where we were allowed to see the remains.)
Brawl Characters not seen yet: Ness, Lucas, Bowser.
Characters never going to be seen: Master/Crazy Hand, Tabuu, Fighting Polygon Team.
Characters with alibis during DeDeDe's murder:
Mario and Donkey Kong: Fighting one another.
Luigi, Little Mac, Pauline, Mr. Game & Watch, Diddy Kong: Watching the fight.
Samus: Present, but not accounted for. (My genre savvy tells me she's a red herring, since she didn't use any blunt weaponry, favoring her stun pistol/whip.)
Some things to think about:
What game characters steal skins/appearances/etcetera? Kirby is one, but he was allegedly being closely watched by Meta Knight.
What, if anything, do the victims have in common?
Is this really related to Zelda and Link's power grab?
Existing hypothesis I've read on Escapist's forum: It's Red, the pokemon trainer. Mostly it amounts to people using genre savvy to point out how much his impossible naivete clashes with the cynical world, how unsuspecting we should be of someone so innocent, and building ideas on that. I don't buy it.
Notes for fellow speculators: Please point out if you have ideas based on genre savvy instead of solid evidence. Citing episodes and timestamps is encouraged.