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Let's talk about some ideas.
I was thinking of bringing back IQ Skills, except with many changes to how they are gotten.
-IQ Skills and points are for your entire exploration team rather than individualized. Any skill you unlock is for all your Pokemon (though they can be individually turned off if you want to).
-IQ points are no longer from gummis. Instead, you get them by completing special objectives in (revisitable) dungeons. Hypothetically, you can complete them all on your first run in-story.
-IQ points can be used to activate IQ Skills. Some of them have pre-requisites. Some of them do mundane things such as increase your team's attack or other stats, belly efficiency, or A-attack power. Others do stuff like Type Bulldozer, point to the direction of the stairs, or even detect monster houses before entering them.
-None of these skills affect AI behavior or anything outside of dungeons.
-IQ points can be re-distributed to different skills at any time outside a dungeon, giving you a chance to experiment, adapt, and regulate difficulty.
-The points you collect from story essential dungeons should be enough to get most of the skills you want by the end of the game. You can try to collect them all to get every IQ skill, but some of those points are from post-game dungeons, including in-story ones.
Think of them like badge points from Paper Mario, except you don't have to buy or find badges, and you get BP from doing extra stuff rather than leveling up.
