Banjo-Kazooie (N64) - I really didnt like it when I first played it when I first bought it - dropped it and re-started about two years later and instantly fell in love with it. I suppose when I first played it, I was going through...a lot - bear in mind, I was like early 10s age. Thankfully I got over what I was going through at the time. I first played the game back in 1998, second playthrough was in 2004 (when i actually beat the game for the first time) and did a third playthrough back in 2017.
Super Mario Sunshine (GCN) - I really disliked the game at first especially since Mario lost the ability to punch. I was also a huge fan of SM64 so the changes didnt sit too well with me at first. Forward at least 5 years later and I did a second run and actually beat the game. I did it again shortly afterwards - enjoyed it the 2nd time and 3rd time. The first time I played it was back in 2002, second time was back in 2008 and shortly after that again in 2010.
Final Fantasy VIII (PS1 and PC) - I really hated the game mainly because of the junction system making magic useless to use (and focus on stats) and the enemy level scaling. I eventually got hold of the Steam/PC version several years later and understood jRPGs and party build ups since. I ended up making a OP party (2 high level characters and a low lv character - also got to use some of my favorite spells but near end game I was using limit breaks all the time) so I actually started enjoying the game finally. I first played the game on PS1 back in 2006 but played the Steam/PC version back in 2016.