@Aaronrules380:
I was discussing this on NeoGaf, but one thing I really want from Pokémon in general (it won't come from these games) is another rival that actually feels like they're competing with you. I get that they don't want to rehash blue, but I think you could pull it off in a new way. I'd like a rival who sometimes beats a gym before you and sometimes after you so you're pretty even. And I'd love a reverse Blue situation where you beat the champion and elite 4 first, but right before you're taken to the hall of fame you're rival appears having beaten the elite 4 and challenges you this time
This!
The fact the player seem to be the only person to ever defeat a Gym Leader bothers me every time I go to a Gym in every game. Like you said, I would love to see my rival got there before me and defeated them. Or after, whatever, but at least at some point.
G/S phone, with random trainers calling you for rematches when their pokémon grow stronger and evolve, is also something I miss more than I should.
But what Pokémon games need the most is a better AI. FFS, everyone and their moms already played pokémon, they don't need to worry so much about new players anymore. Give me a game that needs to me to actually think about the team I am creating, think about strategies. As of now, you just need to pick your favorite mon and keep your team leveled up to take care of anything the game throws at you.
Also it would help if legendaries were stronger, something that would require your whole team to take down instead of just one of them. They could go with the excuse that a legendary out in the wild is much stronger than a caught one to justify that.