Oh yea, i totally get it, it always becomes more linear then planed :D
Doesn´t have to be a bad thing.
Hm... maybe an easy way to give the player the feeling their choices matter is to put visualisations in the dorm room. Like depending on what classes you pick, there could be things related to the choosen topic. Books for american literature, old movie posters for that class related and i have no clue what would fit to computer science :D but im sure there must be things.