That is why you also plop a Dormitory (an option for the University, but NOT one for the Community College) - if you are adding one or more Schools (Business, Science, or Engineering), definitely plop the Dorm.
I usually have the University near City Hall (and Central High School) to ease commuting woes. (I leave space between the Residential and Commercial Districts for Town/City Hall, and the University - the first high school is just south of here at the edge of the primary residential area. Additional residence districts are east and west - like the wings of a phoenix.)
I have found that less is more in this game. I have 0 industry in my factory towns. The factories provide the jobs. As a result, my cities cap at 125k pop but making 2mil a month. The overall effect is less pop, less traffic, less jams, more resources moving around, more profits. What is interesting is that with a minimum amount of commercial buildings, 0 industry buildings, and nothing but factories, I still have a worker shortage. One of the reasons my setup works though is I have another neowin member playing the region with me. I get all my freight for commercial business from his factories and he leeches off my fully upgraded industries like my full nuke plant and 2 recycling centers.
That being said, we are looking for more players if anyone is interested. We have just about everything unlocked for the region other than 2 projects and oil stuff.