Are we talking about underrated in terms of sales or critical acclaim? Or is it internet hype?
I might not understand the discussion exactly, so I'll add a few of mine that seem to be disliked a fair amount, either in general or within specific fandoms.
1.) Star Fox: Assault (GCN)
This game was quite a bit different than SF and 64, though I had a lot of fun with it. I thought it captured the arcade feeling of the N64 version extremely well, even if it missed a lot of what made that game great. 64 is still my favorite game in that franchise, but I found myself replaying Assault a lot more than any other Star Fox game. And the multiplayer was a blast! My brother and I killed so much time playing that while growing up.
2.) Fire Emblem: Path of Radiance/Radiant Dawn (GCN/Wii)
I'm lumping these two together, even if I personally enjoyed the first one much more than the second. I seem to see quite a few forum posters that hate on the localized console Fire Emblems, or a general consensus that the series is meant to be on handhelds (which seems silly, given that the franchise's first handheld entry was Fuin no Tsurugi...the 6th entry). I found the story to be top-notch in the first one (FE9 is actually one of my top 5 video games), and still hold that Radiant Dawn was a worthy successor in that area.
3.) Bleach: The 3rd Phantom (DS)
This might be debatable, since it's based on an anime property, and thus is targetting a select audience to begin with, but I loved this game. It's an essentially an SRPG, using gameplay elements from Fire Emblem and Final Fantasy Tactics, using Bleach characters and an original story that spans several events from the manga/anime (primarily the TBTP and Arrancar arcs). Being able to play as my favorite Bleach characters was a blast, and I enjoyed it enough to replay it instantly afterward.
4.) Golden Sun: Dark Dawn (DS)
This game was a sequel to a two-part GBA series from the early 2000's, and seemed to be despised by a lot of the fans of the previous entries. It might just be that hyperbole seems to overused on the internet, but I don't think this game warrants most of the hate it received. The puzzles were still fun to solve, the music was great, and the dialogue was as entertaining as the original games (though still really long). My only big issue was the Point of No Returns....I really hope those are removed whenever GS4 finally comes out.
5.) The Legend of Zelda: Skyward Sword (Wii)
Whether or not this one's underrated is really debatable...obviously. I've just read enough comments from fans to know this was fairly divisive for a Zelda game. I acknowledge that it was far more linear than I was used to, and the backtracking was a little much, but I don't think it really deserves the hate it seemed to have. I loved the character designs, and the story actually interested me more than I'm used to in this franchise. I think a lot of the hate stems from my hyperbole observation from the previous game on this list.
That's all that come to mind right now. 12 is a bit too much for me. XD
NNID: Zephyr25 / PSN: Zephyr--25 / Switch: SW-4450-3680-7334