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Have you played La Mulana 1 +2 or Environmental Station Alpha?  Those are some of the best games ever made imo and are puzzle metroidvanias.  Puzzles in metroidvanias can often double as "secrets" which really makes things interesting- especially when they involve lore, world structure, or map knowledge as a part of the the puzzle.  

ESA is a very straightforward Metroidvania. The only "puzzle" aspects are in the endgame. For La-Mulana, its puzzles are largely disconnected from its ability/item upgrades, so they don't have this problem.