Lots of useful info in this thread - thanks! I had the opposite problem, I think too many of my students achieve the Honors, even if I don't really make them do anything extra. But I think there might be a big difference between sending a student right from CAS with few skills or cheated skills, and to send students who grew up in game and gathered not only skills but actually lived. I might have graduated 15-20 students, normally 5-6 sims at the time, and saw max a handful bad class grades.
Sims who failed in doing their Presentation (due to the bug where they got the wrong board) graduated with honors. I just had them read a little extra. Students won't need to do everything there is to do to reach great grades, it's the sum that counts - skip project or miss class can be helped by reading up a skill etc.