Except it didn't really come out of nowhere at all. Alternate universes have been pretty much Canon since the fourth generation with the introduction of Giratina, Dialga, Palkia and Arceus. Heck, Arceus even creates an entirely new universe in HGSS just so you can get one of the three legendary dragons of the fourth generation in that game. And even before that it was hinted at, as that was the only logical way that you could explain the differences between each individual game in a generation. Not to mention the differences between the various forms of Pokemon media: The game, the anime, and the manga all work by different rules, but are clearly part of what can best be described as a pokemon multiverse. The only real difference I see between now and then when it comes to the story is that now they actively point it out.
In what world is Arceus creating another universe? All I gathered from playing through the event is that Arceus musters up the power to create a Pokemon egg from pure scratch. There are many implications for this, one I can readily think of is that perhaps this is Arceus's way of keeping Space, Time, and Antimatter in balance should the Pokemon responsible for keeping it in check be caught, or dead. Additionally, we don't know that Time, Space, and Antimatter is limited to one universe, because we don't actually know if Dialga, Palkia, and Giratina have the ability to expand their powers into more than one universe (for instance, Dialga can view past events that didn't really exist in the current timeline etc.).
Also, why does the fact that people have varied playthroughs of the same game/different Pokemon appearing in both games need explaining? Regardless of the different Pokemon choices you make, the events are still going to be the same, and you are still going in the same linear path, so it's not like you're getting something new every single playthrough (as it pertains to story). Lastly, you're assuming that the manga, anime, and games share the same significance altogether and we all know that that's not true. The games are not connected to the anime, and are not connected to the manga because of these very different rules, and vice versa.