I would prefer that they go back to Kanto, and while Ash was away during that time to go to Unova, new Pokemon have decided to migrate to Kanto and stay there. And with all those new Pokemon, Giovanni wants to capture them all and decides to first capture Arceus so it could be way more easier for him to capture all the rest. So at this point, Ash gathers the help of all of his friends that he encountered in each region for their help to stop Giovanni (Who now has Arceus in his power) from capturing the new Pokemon. Legendaries from every region would also come to help Ash and his friends to bring Arceus back to his normal state. The reason why all the legendaries are involved is because Giovanni managed to bring Arceus to a power beyond it's limits and the legendaries wouldn't want to see their creator being mistreated to capture the very Pokemon that Arceus created himself.
The whole plot could be one big huge season to mark the end of the Pokemon legacy.
* Okay maybe this kind of story is too early to put into the Pokemon history for now =P*