FFIV. Not that I disliked it initially, but I actually like it more and more with every playthrough. This became especially noticeable once the DS remake came along, as I feel that version really elevated the game to a whole new level

Another one is FFIII, which was a slog the first time, but once I found Wolf Kanno’s job guide and discovered the awesomeness that is the Geomancer, I liked it a lot more.