This series is amazing.
A lot of you continue to mention that the killer has skill with a blade. Luigi made that assumption, but Kirby told him off because of how wrong it was.
/spoiler
I'm willing to place a wager on the Pokemon trainer as the killer. I've long suspected it, but certain realizations made my mind up. Notably, the Trainer's conversation with Samus was revealing about his worries regarding the kingdom. He's far too innocent for the world he is surrounded by, and probably in an ill-conceived attempt to make everything better, he is killing off everyone who he believes is corrupting the city. With 2 mob bosses among those few that were murdered (Mewtwo and Dee), this seems to be a reasonable assumption at the motivation. Pichu was probably killed off originally just to follow in accordance with the release of Brawl, but they will likely explain it as he had a falling out with the Trainer. Secondly, the Trainer's abilities with his wide arsenal of Pokemon would allow him to easily and quickly commit his crimes. Kirby's final line regarding how close Luigi was to the murderer might be alluding to his literal proximity to the Trainer. Additionally, the first of those murdered was stuffed into a pokeball, and none have been since. This would normally seem too obvious, however, oftentimes murderers commit their first act without planning, leading me to think that a mistake like that is plausible. The disemboweling is probably a message of some kind, or a warning to others, but most likely it serves to darken the plot further.