I can think of many games that even critics ate crow on later and recanted.
Peter Molyneux's "Black & White" was praised as the second-coming on PC for awhile, given supremely high scores and rave critical praise... but a few years later and these very same critics (at least some) apologized for doing so, saying the game was far more flawed than it had any right to be, that much of it was them buying into the hype and overlooking the flaws. It's still considered an okay game, but it's a stark contrast from the universal praise it had at launch.
"Perfect Dark Zero" is another one. Check out the metacritic. The scores are supremely high, and this is still in the post-Halo 2 days of FPS. But it's now considered a fairly terrible game, an amateurish embarrassment to the franchise, and some of the same critics that gave it high scores now list it amongst the worst sequels ever made. Considering its predecessor, that's doubly disappointing.
"Sonic Adventure" is a textbook example. The Dreamcast system-sellar had massive praise and sells, but when it was released a few years later on Gamecube, nearly intact, it was slapped with low scores that criticized the broken gameplay (not the graphics) and terrible level design.
Inversely, I remember reading several middling and low scores for Valve's "Team Fortress 2" at release, with a large portion of critics overlooking it, dismissing it, and calling it the "least interesting" game in the Orange Box, especially next to critical darlings "Half-Life 2" and "Portal". But years of community, study, gameplay, and support later and many of these same critics have actually gone back and either re-rated the game more favorably or confessed they wish they could alter their scores because they didn't "get" the game on their first run. Team Fortress 2 is now widely considered on of the best team-based shooters in existence and a timeless classic with a loyal and passionate community and fanbase. Not bad for the "worst" game on Orange Box.
My own personal feelings on games critics (and sometimes fans) got wrong include the following:
Castlevania: Legacy of Darkness - It's popular to hate on the N64 Castlevania games. They're terrible. Garbage. Yuck. I'd wager most of these people never actually played the game, and even fewer ever played the enhanced update, Legacy of Darkness, for the N64... especially since the game was in such short supply. Basically, it addresses, fixes, or improves nearly every aspect of the original game, doubling the length (and adding two new characters), a wealth of new environments, amazing music, improved controls, towering bosses, a smarter camera, enhanced visuals, a more coherent story, multiple endings, and much much more. I'd actually call it one of the top 5 adventures games on the N64 in the same pantheon as Ocarina of Time, Conker's Bad Fur Day, Banjo-Kazooie, and Rocket: Robot on Wheels.
Two Worlds 2 - This is again directed at most "fans" that have never played the game. The critical reception was actually very high, especially considering how TERRIBLE the first game was. But the sequel is nearly 100% better in every last single regard. Everything is improved: graphics, music, interface, combat, load times, dialogue, voice acting, cutscenes, RPG elements, monster designs, weapon and spell variety, customization, online features, etc. It's one of the meatiest RPGs on the market, period. Is it as good as The Witcher 2? Not even close. But it's also not the abomination many have said it was going to be, or still is, based off of how bad the first one was. I even enjoyed it more than Dragon Age 2... and I'm a die-hard Bioware fan.
Ninja Gaiden - This is my own personal take; I know the people that love this game LOVE it, and it's been showered with worthy praise. I loved it too... and I HATE it. And it all boils down to the difficulty. That's upsetting because it was DESIGNED to be difficult, but my enjoyment of the game is hampered by this design. Nothing is enjoyable about dying five times in a row, going back to your last save point, cutting through waves of enemies, only to die again due to overpowered, hard-to-predict bosses or monsters. But that's okay. That's fine. It's great to have a challenge every now and then. But Ninja Gaiden fails to provide a difficulty mode for casual players. I would LOVE to spend hours of my time mastering and perfecting the nuanced, deep, intricate, and lovingly-crafted combat system to become a true Ninja Master... but I have a job, bills to pay, college seminars to study for, and dozens of other, more easily enjoyable games to play. Just having the option to not be perfect 100% of the time in a Ninja Gaiden game would make me go from hating it to loving it, but it's just not there (even on Ninja Dog). Ninja Gaiden's "normal" mode is harder than most games' hardest mode, and while I can beat multiple games on hardest difficulties relatively problem free, Ninja Gaiden alone makes me rage. I just CANNOT enjoy the game, no matter how pretty it looks, smooth it plays, great it sounds, or bouncy the boobs can be.