I would have to say The Legendary Starfy, I spent an hour playing it, and the whole time I was saying "This has to get better." It's pretty much the same stage over and over again, its really boring. Most gamers hate underwater levels, and a whole game of them just seems like a bad idea from the get go in my opinion.
Personally, I really like TWEWY, but it wasn't that revolutionary. There have been fast paced battles in games before, the only thing it did differently was stylus based combat. While in some cases it may be over-rated it's not over-sold. The fact that most of the acclaim comes from the people who downloaded the rom, because no one wanted to buy it. Low sales = square enix not making another one.
Kingdom Hearts seems over rated too.... I really like the Kingdom Hearts games, but some of the missions are just stupid. Why should I have to investigate everything in an area? It's really annoying to have to do this, especially when you can't find just one to complete the mission.
Professor Layton. I love the game, and everything about it, but it's way over-rated. If there was a lot of good puzzle games out there, this one wouldn't be a top seller. Unfortunately most puzzle/adventure games on the DS are total crap.
Elite Beat Agents. Played it for five minutes and quit. I instantly thought it was stupid.
The original puzzle quest. Sorry, but its just not that great.