Wow! This series is truly incredible! In a world where predictable plots dominate the movie scene, you guys have kept me guessing all this time! Alright, to sum up the speculation and mix in a few of my own ideas:
For awhile, I thought that the killer was somehow Toon Link. The creators obviously went out of their way to reference every character at least once, and he was the only character that wasn't mentioned in the series, although the picture that Link was looking at might have counted, so that's dampened my suspicion. The one clue that I can't get out of my head is Wario's description of the victims. Wario:"They say he disembowels his victims... >>>Tiiny cuts...<<<" That to me has always pointed ato two characters: Toon Link and Meta Knight. Meta Knight would definitely fit the fast killer requirement, although I don't really understand what his motive would be...
The thought that Kirby and MK have the same body could very well mean that Kirby is still alive, although why would Wario kill MK and say he got Kirby? Wario doesn't seem like he has much involvement in any major scheming, and it seems like he hated Kirby as much as the rest of the characters. It would be an excellent plot twist though, so we can't really rule out for sure which one is still alive...
The Master Hand trophy quote makes a lot of sense, but if the creators say that MH won't play much of a part, I guess that doesn't work... As for the info that he'll be older than all the games, I really can't think of anyone besides a central G-dubs or MH. A main GW as the ultimate evil would explain how Ganondorf got his army, although as a final villain, GW would probably not be very intimidating. How would you voice him convincingly? MH could possibly be "older than all of us" if you look at it from the old Smash Universe perspective that MH created all the characters in the first place from trophys/dolls.
Ganondorf just creating the rumors of a greater evil sounds like it might work, although I doubt the creators would go through all the trouble to create the suspense when there's really nothing there. That would just be anticlimactic.
GAH! So many open ends! This is what I love about this series!