The acceptance rate for CSE is a lot lower than the university as a whole, and tough to get in for sure, but I don’t think it’s quite that bad…especially for in-state. My son did not have stellar stats and was admitted in the first round back in October. I think you’re looking at total applications vs. incoming freshman numbers? You have to remember they accept a lot more than ultimately attend.
You should talk to someone at the U in admissions that deals with transfers and they could tell you exactly what you need to do to set yourself up to transfer in. Or just start somewhere like Winona or Mankato. You might find out after a couple years that you’re perfectly happy there and not even want to transfer.