Transfer students! Every character is in school and don't look their age. The idiotic best friend (male). Girls wearing bloomers or extremely short skirts. Bumping into a girl and a face or hand lands somewhere absurdly inappropriate (they fall onto each other in the 69 position. That's one hell of a fall). It's always about school. Does school suck so bad that they have to make ridiculous scenarios? Also, every protagonist "an average, normal student trying to live a peaceful life."
*End of civilization scenario*
"Oh, this store has food in it, but everyone within 100 sq km is dead. I better leave some money for taking what I need just in case the owners body is reanimated and he has to pay bills."
*Epic end of fight scenario*
Protagonist: "You killed my family in front of me and nearly killed me, too. Now I beat you."
Antagonist: "I've learned my lesson. Let's be BFFs!"
Together: "BFF foreveeeerrrr!"
Also, tsunderes. They are overused and just stupid.
"I-it's not l-like I did it for you, or anything... stupid!"
This line is a must with ANY tsundere.
Lastly, Shounen is predictable. Painfully so.