I agree with the message of this image from the bottom of my heart, but dear lord, that "I am 5 years old" typo still has me scratching my head. How old is the OP, actually?

To answer your question OP
• Team Skull were essentially a group of punks who had it out for you and wanted to spite you at every chance they get. Only took jobs if they paid well or had a worthwhile reward. Also had a tendency to wait for you and your partner to get through the dungeon and dungeon boss to then knock you out and take credit for the mission. Got their comeuppance later on and asked for forgiveness, but no siree you punk ass bitches deserve none of that, fucking karma houdini's the lot of you.
• Chatot was just the standard overly-strict authority figure trope you see all the time in anime and tv shows, though I still think he wasn't all that bad. But this part in particular is what drove many people to hate him.

tl;dr Perfect Apple plot was the PMD equivalent to the Bendy episode in Foster's Home for Imaginary Friends.