There are two that stand out to me for being underrated heavily by the critics, and one that seems to be dismissed too much by the general gaming fanbase.
The first critically underrated game, for me, is Alpha Protocol. I didn't run into many bugs (actually, just one that I can think of), and as far as making your choices have actual consequence story-wise, it delivers much more than most games. I've played through the game several times, and it's never been exactly the same each time, due to changing up seemingly minor things. It actually felt less buggy to me than Fallout: New Vegas, yet the latter game gets crazy praise.
The second critically underrated game is Stranglehold. Don't get me wrong, it's not an extremely good Game of the Year contender type of game. It is a John Woo movie put into video game form. And you know what? It totally delivers on that. There was one mission that annoyed me (fucking lasers...), but I didn't regret buying the game (used, of course, for cheap) at all, nor playing through it. It's shallow pleasure, but it is still pleasure, and not a slog.
For the game that I feel has been too harshly slammed by gamers in general, it is Mass Effect 3. Yes, the original ending sucked. That said, I felt the rest of the game was definitely strong enough to make up for it. The party characters were more developed, the chats between characters on the ship felt natural, the voice acting was even more improved from the second game, the romances (assuming you continued one) were extremely heartwarming, and the game managed to be humorous, even when it was by far the darkest game plot-wise.
But nope, the ending sucked, invalidating the rest of the series. And if you disagree with the general consensus of the game sucking, you are objectively wrong.