Just have a few ideas here.
Master hand/Crazy hand would be Mike and Matt Chapman's hands, with attacks like ERASER or something. For the Ultimate Enemy, why not have Ultimate Trogdor? If there was a SS Emissary storyline, how about they go through different dimensions, finding differnet characters? The cutscenes wouldn't have to be anything special, just sprites standing down their with text boxes. Also, for characters, we should have Ultimate Strong Bad, some Sweet Cuppin Cake Characters (who wants to see
EH STEVE! as a final smash?), and maybe some deleted characters? Like homestar winner? I dunno. For stages (I don't know if anyone has said these yet) I can think of Sweet Cuppin Cakes stage and a WEBSITE IS DOWN stage. Also, we should start thinking about assist trophies for cool but minor characters. One idea for an assist trophy? How about "that freakin' duck".
Anyway, that's one I'm thinking for now, please give me feedback on my wall of text.