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Pokemon is complex, ask anyone who's ever attempted to play online, often just spamming the highest power SE move isn't the right answer. The idea that the depth doesn't exist is just wrong, it's there, it's always been there, they just aren't bothering to use it.
There's good AI in these games, the Battle Tower clones in every game are actually challenging at the higher end, so the ability to make a hard Pokemon game.
I recall playing an ORAS hack a couple years back, and the hacker had given a trainer a Baton Pass team. It wasn't that challenging, but at least the trainer had a different strategy, not just pick the move that does the most damage. I'd like to see more stuff like that, there's so many interesting ways to make a team, but you see almost none of that in the campaign.
Trick Room/Weather/Stall/Setup/Terrain/TailWind/Gravity/Hyper Offense/PerishTrap/VoltTurn/etc. There's more than enough Pokemon and Moves to give everyone interesting and unique teams.
If you need to give special Auras to pokemon like SuMo and totems, that's fine, make it challenging.
I'd like to see a generation where instead of type, every Gym Leader has some other kind of specialty they focus. This would remove the necessity to theme every area after a certain type