Considering the story seems to be evolving beyond that of a "child's game with dolls and trophy characters," I don't think it's impossible to say Master Hand got the axe. Actually, he might be in it, but not behind it all.
Master Hand was just the one who controlled the tiny world created through the imagination of a child with dolls and trophies. Subspace Emissary is the physical manifestation of the video game term "Nintendo Universe"('Nintendo' can be replaced with any game series, for reference in the gaming community of a world in a story[game]), creating an entire actual universe where good and bad guys come from all across space, time, dimensions, and spiritual locations to fight, reason specific to each person, but fight nonetheless.
This story is beyond Master Hand.
And BTW: Special Brawl leads me to believe the customization afforded to us in different aspects of Brawl, such as item drops and their appearance. Can you say "On/Off switch for Crates/Barrels?" because I sure as hell can! Not without beaming though. O.o