As some others have inferred, I too find it difficult to quantify an answer to the question of "which school is better?" Too many variables, too many caveats, too much conflicting data. What I can provide, however, are subjective thoughts backed by anecdotal evidence.
-As a practicing aero engineer who spent about a decade working in Southern California, I had the pleasure of working with folks from many different institutions, including UCSD and CPP. What I've learned from that experience is that the quality of employee/engineer is much more dependent on the person than it is the institution or curriculum (assuming a quality institution with a good curriculum, of course). If the qualities that make a good engineer exist in that person (another topic for another thread), then I believe that person can be one...regardless of whether they attended CPP or UCSD.
-As a hiring manager, it's very rare for me to give much credence to the university a person attended...perhaps because of my experience mentioned above. When I hire, I'm looking for a good engineer (again, subjective criteria for another thread). I don't tend to stereotype people from University A as good and those from University B as great...people stand on their own. The only time I will look into a University is if it's one I've never heard of; then I'll check for some type of accreditation and a decent curriculum on paper.
-As someone who might put myself in your son's shoes, I'd look at the choice and realize that I'm going to spend tens of thousands of dollars over the next few years to gain an education. One school will give me what I want, so long as I do my part. The other school might, if they're so inclined, or if a spot opens up, or for whatever goofy motive is driving their decision. To me the decision to your son's dilemma seems obvious, although perhaps my mindset doesn't allow me to comprehend spending that kind of time and money for an uncertain outcome before even writing the first check and attending the first class.
-As someone who once applied to UCSD, I can tell you that I made a decision when faced with an issue very similar to the one your son is currently facing. I was accepted to UCSD, with the aero engineering major I wanted, but was placed in a UCSD "college" with a mission quite dissimilar from my own. (For those unfamiliar with UCSD colleges, see here:
UCSD College System ) When I inquired about changing my college to one more inline with my interests, the answer was "sure, if something opens up in the one you're interested in, you can transfer." Although the likelihood of that happening was probably good, it wasn't worth my time/money to walk into a situation I was unhappy with from day one, hoping a change could be had. My choice? I attended and graduated from UC Davis...and haven't regretted it for one day.