The Legend of Zelda: Ocarina of Time - for the same reason as you. It released when I was 9, and when I was 9, I sucked at video games. By the time Majora's Mask came around, I gave OoT a second chance, and now that I understood the game better, I actually enjoyed it. I still prefered Majora's Mask though, even though I played OoT first and even though you had to save at statues in MM.
.....that's about it off the top of my head. I never beat Link's Awakening, nor A Link to the Past, I'm sure I'd like those games a lot more nowadays.
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I did miss a lot of games growing up, games I just didn't know about which I'm playing one by one. Almost done Lunar, it's a great Sega CD game, and I know Chrono Trigger was something I beat nearly a decade after its release, and it's no my favorite RPG.
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