I've actually wanted to compile a top ten or maybe a top five list of what I found were among the most overrated games in the industry. Off the top of my head, here's a few:
Metroid: Other M - Actually this is an "honorable mention," mainly because it's not overrated by any stretch of the word by its fans. ... mostly. Just the media. I mean it's got an average score of about 8/10 from most media reviewers, making this one of the reasons I don't always trust video game critics. I don't need to rag on this, just feel the need to point out that video game critics are full of shit. Sometimes.
Kid Icarus: Uprising - Horrible controls, repetitive gameplay, terrible dialogue. The actual overall story was pretty good, and the writing and story in the Chariot Master chapter was especially good, but a lot of the fourth wall and anachronism jokes fell flat, and there were just far too many chapters that all felt the same. Because honestly, they were.
The Legend of Zelda: Majora's Mask - This is only of late, but the likes of Zelda Dungeon and Operation Moonfall have made this game even less desirable than it was before. It was a decent game but it had plenty of flaws, and now that fanboys have come out of the woodwork for it, that has really started to tip this into being one of the most overrated games to me.
Halo 3 - I'm a big Halo fan. But Halo 3 was very lackluster compared to its brethren. Storywise it was solid and was an excellent ending to the trilogy. Gameplay-wise... it wasn't as interesting, unique, or varied as 1, 2, or even 4. Sure, it had a kickass escape sequence, but the rest of it was too straightforward and generic. I'll be the first to say that I don't find the level "Cortana" to be as bad as everyone says, but on the whole, the game just isn't as interesting as its peers.