3 games come to mind instantly.
Phantasy Star online episode 1 & 2 - bought it on GC then sold it to a friend a week later, ended up buying it about 3 months after that and loving it.
Monster Hunter - didnt really get the point at first, played it occasionally but took me a long time to hit the 'ah-ha' moment.
Half life - Remember playing half life on PC when i was about 10 years old (in 2000) and just thought it was another mediocre fps. That was until Half life 2 came out and i finally saw the beauty of the series








