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My opinion is that the transition to 3D started the downfall of Pokemon. And open world was the death blow.
The old dungeons had classic staples like
>boulders puzzles
>hole puzzles
>warp tiles
>slide tiles
Just to name a few.
None of the newer games would really blend well with any of these old mechanics because the new games look too realistic. Imagine Juliana or whoever pushing huge boulders and sliding across 20 feet of ice. It would look stupid. The only way it wouldn't is if Game Freak tried really hard and gave us clever new animations or mechanics to make it gel.
On the other hand, the chibi style of the old games worked flawlessly with these wacky old puzzles because the style was so simple and you could just use your imagination. For lack of a better word, the older games are much more "video gamey" than the new ones and we can never go back to that..