As others have said, most all of your concerns are a non-issue with a quality top. I prefer the half doors as well. It was never an issue with mine in the winter.
The only thing I didn't like was the lack of A/C when I went to work in the summer time. Your son, like me, will probably adapt to that so it's not really an issue either. Having a Jeep in college and all that entails will trump the lack of A/C any day of the week.
I started driving the family jeep the day I turned 16 and took it to college. Wouldn't trade those days for anything.