My thoughts:
The last bit was deliciously meta. Personally, I expected Ganon, what with his track record of being the "Man behind the Man", but I would have been satisfied with just about anyone. I do think, regardless of protests, that it was a bit of a cop-out, though. It's the finale, it's not like you have to worry about people catching the next episode.
On that note, why did you have to end it? I freaking LOVED this show, and there were billions of game universes you could have done. And at the rate this got released, by the time you finished a few, sequels of some of the already-done ones would have occurred. You should re-continue it, have someone find the Polybus, and hit the "Reset" button.
...Actually, I'm going to rag on the ending a bit more. What was that deal with Mario attacking Waluigi, anyways? He wakes up, sees a dead DK with a (presumably) dead Peach, and Luigi goes into the room with a plunger? That made no sense whatsoever. Plus, the fight was kinda glossed over. And why did Toad shoot Luigi anyways?
Also, a few questions about how the NPC universe worked (Despite that being a bit of a misnomer). Why did Lazer Cat have to stay dead? After the war, couldn't Shanks have made another game, where a "Lazer Angel" descends and revives him? Or for that matter, make a game chronicling their adventures, with a "Everybody gets better" at the end?
But I digress, for all of my ragging, this has been one of my favorite series, ever. Still wish you'd done more with it, though.