All of these are either underappreciated or outright disliked/hated, and they shouldn't be.
-Skyward Sword has incredible combat and some of the best dungeons in the series. Amazing game and my third favorite in the series behind Breath of the Wild and Majora's Mask.
-Resident Evil 6 has one of the best sets of mechanics in any TPS, and is ridiculously fun to play once you wrap your head around the game flow.
-Final Fantasy VIII is one of the boldest entries in that series, has a fantastic core set of themes that are well-conveyed, and does a ton of interesting and experimental stuff. Also one of the best soundtracks in the series. I truly adore this game.
-Metal Gear 2: Solid Snake is one of the best games in that series, an excellent foundation on which the Solid entries built with a more cinematic and dynamic presentation.
-Dark Souls III is incredibly polished and consistent, and it wraps up the overarching Dark Souls story with one of the best boss fights of all time. Legitimately got chills with the music.
-Retro Game Challenge is a love-letter to the medium of video-games and one of the most notable experiences I've had in the medium. Only a video-game can immerse you so completely in a different time and place - in this case, being a kid in late-80s Japan.
-Tearaway on the PS Vita was a surprisingly artistic game with a stunning ending. Masterpiece
-Puppeteer on the PS3 was one of the best games of the last console generation and had a visual style as striking and bold as the recently released Cuphead (which is also very good).
-Donkey Kong Country 3 is a great game, sure Kiddy's kind of annoying, but Dixie is still awesome, and the level design is still on-point. It stands alongside the rest of the original trilogy as a worthy finale.
-The Yo-Kai Watch games, which I randomly decided to play on a whim and ended up really enjoying, have a fun and unique battle-system and great atmosphere. All RPG fans with 3DS' should try them, they're far more than mere Pokemon rip-offs as a lot of people seem to think.