There have been a couple:

FFII - Didn't care for it initially and then I decided to do an informative FAQ thread for the site and found the game to be terribly more complex than I had first thought. It made me appreciate the game much more.

FFVI - I initially hated it but falling in love with Secret of Mana made me reconsider and I gave the game a more fair try the second time and ended up loving it.

FFVII - I found the game disappointing (and that opinion hasn't really changed), especially considering the hype. The fanbase largely made me learn to really hate it but over the years I've mellowed out and can appreciate some parts of it.

FFX - I originally found it "okay" but a second playthrough made me realize how utterly boring and awful the plot was, how dull the cast turned out to be, and how poorly implemented the game mechanics had been utilized. In fact every subsequent playthrough of the game has made me hate it more.

FFXIII - I intially found it meh, but further evaluation made me realize just how awful this "thing" was and how terrible almost every element of it was. It's the only FF where I honestly am baffled by people actually thinking it's better than terrible. I honestly don't feel it has any redeeming qualities.