First, let me say I really dislike the terms "underrated" and "overrated" because frankly, they're meaningless. People use them as if there's some metric you can use to scientifically show something is one or the other. All it means when you say something is overrrated is "I don't like this thing as much as the majority". Which is fine, but just say that instead, it sounds less...arrogant.
BTW, I believe Bioshock is the greatest new franchise this generation and could expound for hours on why I believe that, but to each their own.
I also wouldn't say the majority of gamers like JRPGs - they are very niche (just look at the sales numbers) and I'd say they're even moreso now than they were 10 years ago. JRPG fans are vocal, that's all.
Now here's a few cases where I differ from the majority:
I hate The Legend of Zelda: Ocarina of Time. It feels absolutely lifeless to me - and this isn't a case of the game being dated, I felt the same when it first came out. Was a huge disappointment to me after LttP. Majora's Mask is by far the best Zelda on the N64.
I also dislike Mario 64. The constant cycle of being kicked out of a world just to have to go back into it really turns me off. I felt Spyro was a far superior series at the time.
Not to just pick on Nintendo & sound like a Sony fanboy - I absolutely hate Shadow of the Colossus. Extremely boring game IMO, just boss fights & empty areas make it feel like a half-finished game to me. ICO I loved, SotC I can do without.
I really tend to dislike "artsy" games - Journey and Limbo are two good examples of this, I didn't "get" either one of them. I enjoyed the gameplay in Braid, but thought the story was hipster rubbish that was completely unnecessary.
Final Fantasy VIII is the best FF on the PSOne. Deal with it.
Chaos Legion is an incredible game that you probably didn't play but should have.
Deadly Premonition isn't good, and it isn't "so bad it's good" - when it comes to games, there's no such thing. It's just plain bad.
The 3D Ninja Gaiden games are wanna-be Devil May Cry's - and they're not as good.
The same goes for God of War.
Coke is far superior to Pepsi, but Mt. Dew is way better than Mellow Yellow.
People who put salt on fruit are communists. Don't turn your back on them.