Star Ocean 2! I didn't realize I didn't have to find a save point, that I could just save on the world map, until like 90% through the game cause I noticed when I was in the menu screen that save was lit up like it was useable. Oops.
Also, the first time I played, I didn't use the feature that empowers your stats on FFVIII, cause I didn't bother to read the directions. Got caught on a late game boss fight and gave up until years later when I finally read the directions and had so much fun save scumming and exploiting renewing magic draw points. (Basic memory from like 15 years ago so I could have some details wrong, but you get the point)