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I can't speak for all of your professors (since I dont know them or what university you are attending) but a common reason why they would skip some of the more common pieces like that is that they are also trying to expand your classical music knowledge beyond the standard the well known pieces. Another reason is that those pieces dont fit into the lesson. Beethoven's Ninth isnt the kind of piece one causally analyzes, one could spend months in class going through that piece. Other pieces like Beethoven's Fifth is simple harmonically but makes for a great lesson on form which are usually left for third year students. As far as the disconnect between between high school and college music, yeah its rather big. High School does not prepare a student for college music.