Arrival at Hogwarts: Because just simply stepping off of the train would be too easy, students have to sail across a monster-infested lake, or be carried by invisible creatures from your worst nightmare. Likewise entrance into the university is strange, unusual and terrifying - whether it be the admissions office, being called for interview or GREs. The arbitrary nature of many decisions that will effect the rest of your life make riding on the back of an invisible thestral seem tame in comparison.
Health and Safety: Classes at Hogwarts often have sometimes the topsy-turvey attitude to health and safety that universities do. On one hand the university requires a 60 page document and committee review for a somewhat innocuous substance that might pose minor health problems, but they don't care about factors that could actually kill or injury - e.g. dangerous field trips, unsupervised labs, serviced minibuses with brakes that don't work, pedestrian crossings that are death traps and (in the US) ensuring students are drunk driving because there are no campus bars or public transport into town (because that would encourage drinking...). Compared to some of the activities at universities zooming around at high speeds on a broomstick at a Quidditch match, seems pretty safe in comparison.
The Houses: Let's face it, all university Departments aren't created equal. Some have all the power players, all the full professors allocations, and new staff positions, better funding for faculty and TAs/RAs, and the most expensive toys. Departments of Conservation/Environment - OK we're Hufflepuff, need I say any more.