I'm fairly critical, so there's not too many on my list, but the biggest one is that I liked Quest 64 (somehow) when I was younger.
I also love La Mulana 1&2, along with Deadly Premonition, though those are more "cult hits" aka critical failures that 'widely disliked'. But, I'd definitely hesitate to recommend any of them to someone unless I thought they'd be into it.
I really liked Star Fox Zero and think it's one of the best games on the Wii U (which is basically an entire console of underrated games). Fly and drive fast, blow up cool robots piloted by wacky furries, find secret exits that form multiple game paths, do fucking BARREL ROLLs - aside from one level which is really slow and sucks, Zero should have been everything people wanted
Oh but apparently it's "too hard" to fly with a joystick and aim with the gyro, and instead of getting good the game community completely rejected Zero based on its controls. I'm reminded of how the first games that used twin stick controls got bad reviews for them despite it becoming the gold standard once people got used to it.
It just sucks. We had to wait like eleven years between Assault and Zero, and it'll be at least eleven more before Nintendo takes another risk with the franchise, which along with F Zero (last game released almost 20 years ago RIP) is one of the best IPs Nintendo owns.