As much as I wanna see a normal Pokemon League with Ash actually winning the thing, bringing Team Flare into it would certainly make it more interesting! That also means Alan would come back into it, and I am also all for that.I personally think the League will be interrupted and Ash and them will be traveling all over the region to stop Team Flare. This might be the reason why the Pokemon League will be held in Lumious City. Which Ironically is where the Start of the anime, middle of the anime and the end of the anime will probably be.
They'd probably have some league battles, Team Flare getting in the way, and then more league battles until Ash loses and it ends.
Or Team Flare decides to move into a Alola, and Ash follows them there. Only Ash, because Serena's Showcases are significant to Kalos (that we know of), and Clemont's gym is in Kalos obv.