Seconding FFXII, Animal Well, and Slay the Princess.

Dragon Age 2 was a rushed game but it's still BioWare at the top of their character writing game.

Rule of Rose is definitely not a 6/10 game.

I’m struggling to tell if this is satirical lol. But aren’t The Witcher 3 and Clair Obscur among the highest user and critic rated games of all time on MetaCritic? And weren’t they the winningest GotY titles of all time at the time of their GotY season?

It's still not enough. 

Final Fantasy 8, my favorite game in the series. Favorite RPG period.

Bayonetta Origins as well.

Kid Icarus Uprising
Wonderful 101
Starfox Zero

I feel that most games that try a unique control scheme get unfairly criticized because new control schemes feel awkward at first, because they're new.

Well I guess that’s a fair point lol.

Also indies are pretty much all I play these days and I feel most are underappreciated.

I really tried to like Wonderful 101 but I could not manage to draw the correct forms in the heat of the moment and it was so frustrating.

Kind of my point. Takes practice. Just like the first time you played an FPS you probably kept walking into walls. But since it's new and awkward at first people conclude "the controls are bad" and put it down in favor of something more familiar. Of course, everyone is entitled to spend their free time how they like, but I think this attitude disincentivizes developers from trying anything unique in terms of control schemes which is disappointing for me as someone who likes that sort of thing.

Also if you were literally drawing them on the gamepad, using the right stick was much better.

A few more "mainstream" (not really, but in a way they are) cases: Metroid Other M and Golden Sun Dark Dawn. People HATE these games with passion. And to me they are great! Not perfect by any means, but they have a lot going for them.