When I was about 10 or 11 my friend got me Super Metroid for my birthday. I tried it once or twice, got lost near the start of the game and stopped playing (I was a stupid kid).
I didn't play the game again until December. I finished it this week. Now it's one of my favourite games ever (it's definitely in my top 5 games).
There are a couple of other games that I didn't like at first but now consider some of my favourites:
Starfox,
Super Mario Land (I'd played 6 Golden Coins first so this one seemed dated)
Tetris (boring to a kid)
launchpad25
For me, I wouldn't say there were games that i didn't like at first. Just games i probably didn't pay attention to at first, but tried them out years later. Then there are games that probable didn't appeal to me then, and still don't appeal to me now. Getting back on topic, i'd say that the 'Mega Man' games are my pick for this topic. I liked the originals, but could never get into the 'X' series, or any of the later spinoffs.