Oh God, could you please share how you got the good ends?? I only achieved one with Jonathan!
(I copied and pasted this, because I just answered someone else's similar question)
What I did was choose all of the "polite" dialogue choices, sat in the front of the class, stayed after class to talk to Jonathan, then stay during lunch. Then, I chose not to hit snooze so that I could get to class early and talk to Jonathan again (Tell him that you came to report back on the mission). When he talks about how boring he is, tell him that there's nothing wrong with being boring, and then when you get to the beach and sit down with him to read a book, tell him you're smiling because you're happy. At the football game, tell him the truth, and then later on, tell him you came because you wanted to spend time with him. That should be it! :D