At Susquehanna, we are just wrapping up scheduling for Fall classes and let me tell you: it is not the easiest thing in the world. Things never seem to go for you the way you want them to. You always start out with a plan for your Fall that you think is foolproof. You know every class you need to take for your major(s) and minor(s) and what you want to take for fun and then... you get the newspaper with the times and days of all the classes. You find out that all of the classes you need to take conflict with each other because they are all at the same times. All of the classes you wanted to take for fun will have to wait for the next semester because you now have to move your schedule around for the classes you are required to take.
Another difficulty of class scheduling is the fact that some classes are only offered during certain semesters or years. Where as some classes are only offered in the spring or fall, there are classes that only come around every two or four years, making it impossible to retake if for some reason you fail or can't take it in the first place. I, myself, am having some issues because I am going abroad for a whole semester. While I am away there are two classes I need to take that aren't going to be offered again until after I am supposed to graduate. I had to do a lot of reconfiguring in order to make sure I could graduate on time.
A third thing that makes class scheduling really difficult is the fact that all of the departments schedule classes at the same time. So the classes for my minor and major are sometimes at the same time. This semester the class I have to take to fulfill my minor was at the same time as a class where you just get to read and I am an avid reader so I am really bummed I can't take that class. Scheduling has always been a long, and grueling process, if only it could ne easier.