I'll just go with some exclusives from each hardware manufacturer along with some 3rd party franchises to balance things out:

Nintendo:  Pokemon, Splatoon, and Animal Crossing are highly overrated.

Microsoft:  Halo after the first 2 games and Gears of War are two of the most overrated series in gaming IMHO, and have been even more and more disappointing with each installment.

Sony: God Of War, Uncharted, LBP all highly overrated.

3rd Party:  Metal Gear, Crash, Final Fantasy + about 95% of JRPGs.

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. 

Never looked at it in that way. You have a point. But for me, the whining baby it's enough to not enable me to see all those great things. For me, a masterpiece must be almost flawless. And that mechanic is, my friend. a big flaw.

It's not a big flaw at all.

If you don't like hearing him cry, you simply need to get better. The mechanic and annoyance that comes with it urge you to quickly react and find ways to make it happen less. And once you finally get good at the game, you barely hear him at all.

This is yet another example of "This feature of a game doesn't bother me very much, therefore it shouldn't bother anyone very much". It's just so narrow-minded.

Let's try another example to get the point across.

"Find the hovercraft levels annoying in Battletoads? Bullshit! That mechanic is perfect! It's not the game's fault that you're just shitty at the game for not literally memorizing patterns and executing perfectly in order to beat it!"

Horse. Shit. Some people to this day have refused to touch Battletoads for decades because they were never able to conquer that stage and couldn't care less if they ever do. They're not wrong to feel that way. That game was unmercifully hard to the point where it became intolerable for many people.

Video games are supposed to be fun. If some part of a game isn't fun for you, that's entirely valid. If it makes you not want to play the game, that can definitely be considered a flaw of the game. If it's so annoying you would rather never play the game again than deal with it? It can be considered a huge flaw.

You're going to have to come to terms with the fact that other people can have perfectly valid opinions that you don't hold.

Sounds to me like someone really pressed your buttons. 

If you actually read what he said, then you would see that they gave perfect gameplay themed reasons why the whining baby mechanic was actually important and how it worked. 

The Aesthetic and theme of the game are that Yoshi is escorting BABIES to their parents, protecting them along the way like a mother would. From an evolutionary standpoint, the sound of a crying baby is supposed to trigger the instincts to care for said baby, and the frequency and tone are both pitch perfect to get parents to leap into action. This game is emulating that, using your desire to care for your baby as incentive to teach you to get better. 

Therefore, from both a thematic and gameplay standpoint, the whining baby makes perfect sense. 

It sounds to me like you're just upset that someone else found value in something you dislike. Either that or you suck at games and the crying baby never stopped for you, thus enraging you to the point of frustration instead of having the desired effect of having you...

....in the words of a Dark Souls player...

Git Gud. 

(To clarify, I absolutely hate that damn baby, but from both a gameplay and thematic standpoint, it is a great mechanic. That is the difference between objectivity and subjectivity. Don't try to use the difference between those two to devalue one's argument, it will make you look like a fool.)