I have not yet played the game myself, but I have to say; What did you people expect? The original Galaxy didn't even manage to work out an internaly consisten plot - which, for the record, for some reason included time-travel, parralel worlds and a massive deus ex machina to cover up that left-field end of the world routine before the end credits rolled. I'm still not sure about the paradoxial nature of the ruined Starshroom from the past universe and Rosalina apparently being her own mother... Frankly, the game, for what it is - and I get what Koizumi was going for - isn't particularly well written (but it's still better than Sunshine - shame on you for that one, Koizumi!). I don't blame Miyamoto if he wants to cut down on that.
Still, I don't think this intro is very jarring considering Galaxy made it painfully obvious that a new universe was created (with some differences to the original) and that there are infinite number parralel ones - one of which presumably acts as host for the events of this game.
And story is a secondary, incidental concern for Nintendo (if that wasn't obvious already). Less is definitelly more in this case.