Sounds interesting to me. I find real-life examples are usually helpful for understanding things.
1. Some courses were too easy and I thought I was wasting my time and considered applying for exemption. By the rulebook, only students who have taken similar courses in polytechnic were eligible. Projects I did on my own time that was more technically advanced than coursework, were not even considered as basis. Attempt to negotiate with professor to work on interesting/new/hard project (that will show my skills and understanding of subject) in exchange of exemption from boring coursework didn't go well either. (Hey, it is not about grades, it's about challenge and doing interesting work.)
2. Computer Graphics course, homework is to design animation of one 3D shape morphing into another one, but scene must be defined as parametric equation (x,y,z,t). I did it with PovRay, submitted scene source files and rendered avi file, but it wasn't accepted because I didn't do it the "right" way, which is to use special extension to VRML our professor developed. So I needed Windows to install extension to VRML plugin for Internet Explorer. My argument of "students should have choice on tools to demonstrate their understanding of theoretical concept" didn't go anywhere and I got zero for doing it with povray.
3. I was not happy about requirement of "GPA in top X% of class" to get into undergrad research program. I tried to get around of it with simple hack, if I could convince a professor there will be exception to that rule. Wrote a long letter to 4 professors explaining about myself, attached the abstract of research I was planning to do. All replied and met with them to talk about it. Learned that they don't have any influence/power on selection of students. Later e-mailed to who was responsible and got to quick and short NO.
If it were not my laziness, above things shouldn't have happened in first place. What I mean is, I don't want to sound like I am completely right on all situations here, I am just telling some anecdote stories about NUT syndrome I witnessed. Am I being unreasonable for expecting special treatment from school? They all sounds like common sense to me but answer was no every single time I asked something outside of the rules.
Being a product of the same education system, I can empathize. However, things have changed and I know of very different experiences. Although there exists rigidity in structure, administrators have become much more flexible and don't expect the same deference to authority that might have existed. Here are a couple of examples:
1) The story of how CS3216 got started in NUS is classic: http://www.comp.nus.edu.sg/~cs3216/
Students knew of the recently started Facebook class in Stanford and thought it was a great class to have in NUS as well. They wrote out a proposal for the class. They approached a few lecturers in the CS dept before finding one sympathetic to their needs. He committed to teaching the class. They refined the proposal with him. Then they went to the Dean and over a pizza, gave him a well thought-out proposal for the course, got his approval and further edited and refined it with his input. The course was implemented immediately the following semester. The pace of getting it done is definitely not usual but they did it.
2) From personal experience, having gone on a year-long exchange program, I came back to find that certain modules I had done overseas were not all mapped back, which left me having done extra modules which didn't count anywhere and still one short of graduating. I went to the relevant authorities - sent a bunch of emails and had face-to-face meetings. Initially, I was told by an administrator that it was impossible and I would have to do an extra semester. I smiled at the person and changed tack. I figured out ways that the school could map the modules I HAD done and approached someone who could approve that. Eventually, I got the module mapping accepted and I graduated without wasting an extra semester.
My takeaways: 1) Look at your problem from their point of view - the extra administration it would require etc. This will lead you to 2.
2) Don't just show up with a problem. Do your research and propose solutions to your problem. If you ease the thinking required by the relevant authority, it will help ease your approval process.
3) Don't take NO for an answer - especially if you think you're right. Change tacks if one approach does not work.
4) Communicating properly helps a lot. Always start with deference and build a relationship before presenting your problem and solutions. They'll find it a lot harder to turn you down.