The Palace of Shadow and the Soli-Tree are honestly my favorite final dungeons in the Mario franchise. They have a very unique, unsettling, and foreboding atmosphere to them that doesn't feel like any other location in the Mario franchise.
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I haven't played all of them, but IMO most Mario RPG final dungeons are pretty linear and don't challenge the player enough for being the very last part of the game. I have to agree with your choices tho