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battle frontier, pokeathlon, world championship/tournament matches with brackets & random elite trainers (attendance dependent upon league level + time/season of the year), contests, vs seeker, gym + e4 rematches, receive a random out-of-region (otherwise unobtainable) pokemon egg from another established region as a reward for winning certain battles, season cycles, an actually interesting/fun game arcade (bring back voltorb flip too), more doubles battles. oh yeah, and make it a proper rpg where you can actually influence elements of what happens in your story, rather than simply arriving at a predetermined destination to win another battle.
in short, cram all the replay value you can into 1 game.
oh, and this is just an errant thought, but i think it'd be devilishly neat if you could "retire" a character in a playthrough with whatever team you wanted, start a new playthrough, and then wherever you parked your last character would be where you could have a battle against yourself. the obvious problem with this is that you could delete all of that character's pokemon moves before you overwrite that save with a new one and then have an easy way to level up your new party, but i think this could be mitigated by simply granting 0 exp/0 evs for fainting your old character's team. it would simply serve as an elegant, romanticized battle between the old you and the new you.
oh, and for the love of god go back to 2d. ok, that's it, i'll keep the rest of my shitty opinions to myself.