Vanquish is definitely the best TPS last gen (doesn't quite beat Resident Evil 4 overall though) and Ghost Trick is definitely criminally underrated.
Anyway, I'd also like to mention...
Now the game itself sold over a million, but even then I don't see it mentioned at all beyond the series enthusiasts.
Punch Out (Wii) is honestly the secret best game of last generation in my honest opinion, if we're not counting handhelds. (My previous mention, Elite Beat Agents, takes the cake otherwise.) I seriously can't find any flaws in this game. None. It's very, very solidly designed and the mechanics are extremely tight, and it's a game that just keeps you at the edge of your seat so many times.
Punch Out at first glance is a boxing game, but it's really more of a puzzle game if anyhing. However, it captures the essence of boxing perfectly. There's this feeling of nervousness when you're 1 to 1 against your opponent, but you're also determined to beat them. It's intense, it's personal. It captures that element of boxing very well.
Punch Out is all about quick adaptation and learning, you have to figure out your opponent if you want to win. That's another element of boxing capture well here. You have to be precise and time your dodges and punching right, and it's an incredible feeling when you got that three stars on the top of your health bar.
Seriously guys check it out. It's amazing.