The two that come to mind the most in recent memory is FFVII which I initially liked but wasn't floored by, eventually grew to hate it, and I've since kind of came back around to my initial feelings about it. Good but really flawed.

Xenosaga Episode 3 is an entry I initially loved and praised as the best entry, due to nostalgia and being surprised I finally got my ending to a series I thought would die with the second entry, and now I feel it has way too many problems. I still enjoyed it, but with the Xeno love subsiding, its much easier for me to see the glaring problems with the game.

The Kingdom Hearts franchise is another I've gone back and forth with, but trying to replay the franchise from the beginning in anticipation for KHIII, I can safely say I fell off the bandwagon and have no real intention of ever getting back onto it. I know KHIII left the series with more mysteries to resolve, but much like Bleach at the end of the Aizen Arc, I don't really feel like the world needs a KHIV or even a spin-off title. Let it end.