With the leap to console and the increased space that brings I'd like to see the first 'non-handheld' main franchise game be the actual send off of the handheld franchise. If they'd like to reboot it there's one last thing they need to give us first. A global pokemon game. All seven regions on one map, the ultimate road to the champion title. Fight your way through seven leagues, seven elite fours, earn the title of World Champion. Be the very best like no one ever was. Along with this we are talking add every pokemon to those regions, all the regulars, all the legendary, and for each regional dex completed, the mythics. Make it possible to catch 'em all. That is how you send off your series.
The storyline is pretty simple. You are a bright young trainer working with a pokemon professor studying regional variants that have cropped up (so instead of new pokemon there would be a handful of 'variants' in each region). Alongside that, the newly formed 'World Pokemon League' is putting out the call to all trainers to step up and see who will be the first World Champion. As you young protagonist, begin working your way through the game, you discover a shadowy organization that is infiltrating the League, looking to corrupt it for their own uses. Can you complete your research, stop the evil Team Thoseguys, and become the very first Pokemon World Champion?
^ After something like that they can reboot to their hearts' content. They can release whatever new pokemon they want, keep whatever old pokemon they want, and change things up into brand new open world shenanigans or whatever seems most fit to them. But make that last game so very over the top that everyone knows the era has ended and we aren't even mad.