Well, I have enjoyed many games that Yahtzee thinks are shit, but that's not really the same as disagreeing with him. What games he likes are up to personal taste, just as my preferences are, so there's nothing to argue about regarding that.
But there are some opinions that Yahtzee holds regarding general gameplay and game design that I could hold an argument over. It is important to remember that he always exaggerates himself for comedy's sake, but he has made it clear that a lot of what he says in his reviews and his column are opinions he truly does hold.
For example, Yahtzee dislikes cutscenes. Any time that control is taken away from the player in a player-driven medium, he says, it is a bad thing and something developers should avoid. That is not always true, as there are several uses for cutscenes to enhance the game. Just because the player is not in total control 100% of the time does not mean the parts where he loses control are flawed or inferior. Story-driven games especially can benefit from cutscenes, if they are not too long, not too boring, and are the most effective way of delivering the plot.
Also, quicktime events are not pure evil. There, I said it. He even says himself in the Uncharted review, I believe, that they are as fair a way to get through a cutscene as any, as long as you make them a core part of gameplay. So, games like RE4 which contain many QTEs, and is not usually punishing about them, should not be derided for their use.
And I don't really get his issue with third-person cover-based shooters. He seems to think they are designed as simple pop-up shooting galleries, which some of the bad ones might be, but it is ridiculous to think that it's an inherently inferior genre. I've never actually played one that didn't have some form of battlefield control, such as strategic use of cover positions to flank enemy squads and flush out entrenched foes, or special powers a la Mass Effect to get around fortified positions. It is no less legitimate and strategic a genre as first-person shooters, it just relies on a separate cover function instead of strafing around corners.