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Ideally? Full 3d with free camera, cities would have a layout like the johto redrawn pic you posted but without all buildings having to face the same direction, and more realistic proportions. The games should have a cohesive artstyle without ugly low res texture stretched infinitely, and should take advantage of not so modern 3d techniques like materials, bump maps and roughness maps so everything does not look like painted plastic. Routes should also follow a realistic layout that makes sense and does not feel unnatural. There should be plenty of open spaces with interesting landscape worth exploring, but not empty wastelands of nothingness.
Pokémon should roam said open spaces (aka their habitats) following behaviour patterns that are consistent with how their specie is known to behave (IE some Pokémon run around, others stay hidden in the grass or in trees, some live in packs, etc. Basically what we see in New snap).
More in general: good skyboxes, LODs, and atmosphere. Every region should be consistent and unique, instead of the 69 different biomes bonanza that we've seen lately.
tl;dr
Ideally Pokémon games should simply look good.
