This might be an obscure example but I'd like to see a Pokemon puzzle game similar to The Adventures of Zack & Wiki. That game is about going through levels with a treasure chest as the end goal but the chest is guarded with several tricks and traps. The protagonist possesses the ability to turn living beings into items and uses said power to solve the puzzles (like turning a snake found in the level into a grappling hook to reach something).

I've been thinking that a game like that could be pretty easy to adapt into the Pokemon world. The protagonist could possess the ability to temporarily befriend Pokemon (like a Pokemon Ranger, but this spin-off wouldn't be about drawing circles) found in the area to help them solve puzzles or get to places a normal human can't reach. I suppose it sounds too similar to HMs and Ride Pokemon when I type it out now but I'd like to imagine the concept would be executed on a more creative like Zack & Wiki did. A Pokemon trainer protagonist could work too but they'd have to balance the puzzles around the fact you could potentially bring over Pokemon from past levels.

Aside from that, a Pokemon farm or gardening game like Viva Pinata is what I always wanted.