OK, after thinking hard and being inspired by Black Ops 2 I thought of some missions which have an effect on your standing with other kids.
Below is fake, but it's the best I can think of off the top of my head
Example: The Setup
Ben (Protagonist) is walking around Bullworth, trying to get to know the grounds better.
He sees a group of rough-looking boys staring at him.
He picks up the pace but is stopped.
"Hey there pal..." says the kid with blond hair.
"H-Hey." says Ben.
"What's your name, sweat stain?" asks a spotty brown haired boy.
"Ben. I'm new here" says a slightly scared Ben.
"Do you know what we do with new blood?" Trent.
"Uh.... no?" Ben
"Well, your gonna find out...." Ethan
"Wait!" Wade "Because he's new he could help us with our Thad problem"
"What's a Thad?" Ben
"You shut your mouth." Davis
The boys have a quick discussion.
"OK new kid." Trent. "We need you to run a little errand for us."
"And if I don't...." Ben
"We'll keep you here and beat you to within an inch of your life" Wade
"Now, go to the library, find a guy named Thad. And bring him here." Davis.
"What's in it for me?" Ben
"We won't hurt you for now." Trent.
"Bring him here by 7pm. Or else new kid."
"OK..." Ben
Mission objectives:
Go to the library
Ask around for Thad.
Find Thad.
*CHOICE*
Escort Thad to the basement before 7pm.
OR
Warn him about what the Bullies are doing.
Escorting Thad to the basement will result in the Bullies leaving you alone for a while and you will lose Nerd respect.
Warning Thad will result in the Bullies coming after you, but increase your Nerd respect.
If choice one (Escorting) is done, the chapter storyline slowly evolves into being the Bullies little errand boy.
If choice 2 (Warning) is done, the chapter storyline evolves into avoiding and helping the Nerds defeat the Bullies.
Possible rewards:
1: Nerd respect: -20
2: Bully respect: -50 Nerd respect: +10 $10
Just a crap idea, but how'd storyline dependant missions sound?