I think it is absolutely an issue of level design. No one forced Game Freak to make parts of Hoenn's Victory Road pitch-black, for instance. Kanto's Victory Road was fine without that, both before and after Ruby & Sapphire. And I don't even think HMs were always bad - they're handled just fine...
I think the basic idea of a Final Dungeon before the League is good, but they do somewhat over-rely on caves to help fulfill this purpose. In Sinnoh, I find this particularly bothersome, given how much of the rest of the region was already mountainous or cavernous, and looked the exact same...
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