Open world, where you start in the middle of a big map or something, and you can then go in any direction and do gyms or dungeons or whatever in any order you wanted. having all pokemon be attainable somehow would be great, and all the old legendaries could be found through some new quest structure which would break up the traditional gym battle sequence.
Maybe there could be some advantage to specialize your team, like how every gym leader sticks with one type despite how vulnerable that team is. Maybe if you built an all fire team, then there would be some synergy system at play which would give you some benefit to compensate for the lack of diversity.
Speed up battle big time. B/W was an improvement over D/P, but still so so slow. I shouldn't have to wait ten seconds for a chansey's long ass health bar to drain after a critical hit. A big thing would be the option to turn off the "wild rattata appears! go weedle! *weedle makes a sound*" sequence.