Probably Yoshis Island. Its a beautiful looking game, but it just have some really annoying gameplay mechanics.
I have a gigantic list of games that everybody seems to love and I think that are overrated, but I'll go with Yoshi's Island too because it's the type of game that I like the most (Nintendo platform games), yet I cannot understand why everybody praise it so much. Even worse: why call it Super Mario World 2? Super Mario World truly is a masterpiece. Yoshi's Island? Nope.
I just recently beat Yoshi's Island and did a completionist run (100 on all levels, including the bonus levels), and I can say without hesitation that it might be the first game in Nintendo's long-running history that kicked off the idea that every single level in a game introduces a new mechanic or idea, and that - alongside its crayon aesthetic - puts it well ahead of its time.
The game controls flawlessly.
The game looks charming even to this day.
The game's level design is progressive in many ways, and every level is in some way or another unique. One level introduces fuzzy, another focuses on rolling rocks, another has poochy, etc. As the game progresses, new ideas and themes are introduced, and the game is better for it.
Sure, the whining baby mechanic is just the worst, and there are some elements of frustration throughout, but to say it's not a masterpiece is a little misguided.