Perhaps I should clarify, my university has a system based on year admitted to the university for registration. Seniors go first, then junior priority, then juniors, then sophomore scholars, etc. Priority registration is for those in the Scholars program, (which is full-tuition or full-ride scholarships and the priority registration is one of the perks), student athletes, and Bonner scholars (who are required to volunteer something like 10 hours a week I believe, so they need to schedule their classes around that).
Also, for some courses where there is more likely to be a variety of class standings trying to sign up, the classes are set up so that the caps increase as registration continues. For example, some of the dance classes start out with a cap of 4 for seniors, then 8 for juniors, 12 for sophomores, and then the cap is raised to a total of 16 for freshmen registration.
The first-year seminars have a cap of 6 for priority registration, which is then increased to 16 before regular freshman registration. I couldn’t get into the course I wanted because the 6 spots went really fast during priority registration (within 6 seconds), and during regular registration, the wifi crashed for a good minute, meaning those that were on desktop computers took the spots.
So overall, they’re pretty good at making sure priority registration and/or class standing doesn’t lock you out of courses. It just doesn’t help if you’re trying to sign up for courses that are normally taken by those with a higher class standing or in departments where they are understaffed and can’t have enough sections to hold everyone trying to register.
While it might seem like a lot of students when you add it all up, these students are not all taking the same classes so it makes it very unlikely that classes will fill up with just the athletes and honors students. Classes (as far as I could tell, and to be fair, I did not patrol every class offered at my school, but I was in a very big department where every major was impacted) never filled up with just the priority registration kids at my school. Some classes would fill up with the first wave of students (who had senior standing), but obviously, the vast majority wouldn’t.
There are a lot of tricks to making sure you’re making your way towards graduation. Sometimes, you have to take classes at a bad time or with a bad professor. Sometimes, you have to take a class a semester earlier or later than you wanted to. You should register right when the registration time opened, and you should have a plan for exactly what classes you want to take (and a plan B or C or D if you want to take a lot of popular classes). You can waitlist and often get into courses. Sometimes, you can get special permission to add on a course. If possible, try to take all of your core courses earlier on in college when you can be more flexible in case times conflict or a class is full or whatever. Take electives last because then you can have the flexibility to take a different class if you have to. Registration can be a game, but it’s not an impossible endeavor. No system will please everyone, but be real, priority registration is not the reason that students aren’t getting into all the courses they want.
The effect of athletes depends on the size of the school relative to the number and size of the sports. While some small schools may have 40-50% athletes, a big school may have only a few percent athletes, because the football, basketball, rowing, lacrosse, etc. teams still have the same number of athletes.
Back when I was in college and registration was done on paper, the school allowed departments to prioritize enrollment into their classes by major, class standing, and class level. In addition, during pre-registration, students would only get higher priority for a portion of their courses (it presumed that the courses you listed first were your most important ones, so it would give higher priority for the first N credit units of courses listed). It seems surprising to me that so many colleges today do registration strictly by class standing, which gives the school and departments less control over ensuring that available class space goes first to those who actually need the class to stay in sequence for their major. Doing it strictly by class standing basically says that seniors looking for out-of-major electives can crowd out frosh/soph/juniors who need the class in order to graduate on time.
While many may do registration by college credit, some of the more popular majors may restrict some courses to majors only or hold spots for lower classmen in the major. I know at my school, some departments had lots of room so they didn’t have to restrict any classes. Others made it so that freshmen or majors only enrolled first. Some made it so that only makes could enroll in the course. Others required you get department approval. Some colleges use a two pass system to help lower classmen get more of the classes they want early on. Many colleges and departments handle this problem in their own way.