If middle school students created school, I would imagine that they would create a setting different than what the average student currently experiences. Students would want the freedom to choose who their teacher is, frequent snack breaks, extended mental breaks, one to one technology and flexible seating. They would also have control over what classes to take as well as where - many would appreciate learning in the real world with on the job training. Bottom line, student choice would be at the center of this school.
I would envision that teachers would be responsible for choosing the classes offered, but student input in regards to specials would definitely be accounted for. I see this specifically being true of those who are interested in learning a trade and they will therefore be allowed to do so. We would either have experts come in and work with the students or perhaps students will complete their learning off campus. In regards to your last question, a teacher would offer the same class multiple times a day, which should allow for a higher number of students to take the course.