I agree with Shauna for the most part, as people with complaints tend to be the most vocal and over time they usually move on to other things and leave the people who enjoyed the experience behind; there's also the subject of knee jerk reactions, something I am horribly guilty of, which subside over time and leads to fairer re-evaluation of a title.

Games I can think of that public opinion has totally flipped on are:

Final Fantasy VII, which has gone from popularly adored, to popularly rejected, to a little of both on the fringes but overall fairly evaluated.

Mario II, which most people seem to like now, though when I was younger it wasn't especially well received, and once Mario 3 hit no one wanted to touch it, even though Mario Bros. and Duck Hunt remained a staple in their NES library.

Every single Pokemon generation that isn't Gen II, which will be widely heralded as both the absolute worst and one of the best generations Game Freak has released at least once.

Super Mario Sunshine, which everyone I knew hated when it released, but people in general seem okay with now. At the very least far more than when it released.

Wind Waker, Zelda II, and Majora's Mask were all generally unpopular with the people around me when they came out, for varying reasons, but now all three are quite popular and loved titles.

Why are most of these Nintendo titles? >.<