A while ago, I saw some articles about Brawl's story, and eventually, me and others who played the story mode came to this conclusion: It is about a child who is growing up. Master Hand is the child, just wanting to play with his toys - the trophies. Tabuu is the kid growing up. Playing with toys is childish, and as such, TABOO for an adult. So, he takes the worlds and locks them away in a sense as memories of his childhood. He puts away the toys (they turn into statues to represent this). Eventually, the urge comes to play with them, but he resists and locks all but a few lost ones away (the ones that Dedede's timers were on). Master Hand is, of course, gone. Eventually, the adult goes back to play once more out of nostalgia's sake. Snake being there is explained by the fact that, since he's gotten older, he's embraced new things.