I can name four Metroid games I love, and one of which is my favorite game (Prime!). But I think Zelda has a more substantial streak of quality experiences and I can name five Zelda games I love.
Bear in mind that I'm not comparing the gameplay or superficial aspects of either franchise, because that is an necessarily complex way for me to decide which one I prefer.
So I say Zelda. If it were solely between my favorite Zelda games and my favorite Metroid games, however, Metroid would win handily. On an unrelated note, Xenoblade versus the best Zelda games is something I suddenly want to ponder.
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