I had a tough time getting into Witcher 3, I stopped 2/3 hours into it. Restarted it a few months later and completed a 100+ hour playthrough and it's in my top 50 games of all time easily.
Ocarina of Time would be another one, never had it as a kid. Tried to play the n64 version later and just couldn't last more than 2-3 hours, the frame rate makes it unplayable for me. Wasn't until I eventually tried it on 3ds that I realised what a well designed game it is.