I had a similar experience interviewing there. I think you hit a lot of good points.
The USC guy (Mittelman) was alright and I think he'll be good for the program, but I really did not like the Caltech program director (Mazmanian). I asked about the long graduation rates (I talked to a student from his lab the night before at dinner that was finally going back to USC after her 7th year in PhD) and he got very defensive. So I would avoid that topic if you do interview there. I also noticed a lot of students did PhDs in topics not related to whatever medicine they wanted to do (one of them was working on a solar-toilet?), and he argued that it was more about teaching them to be a "Caltech quality" investigator (which is somewhat fair but if it's going to be 7 years of something completely unrelated what is the point of the MD/PhD program?). I agree that not all the students seemed all that thrilled with the program, and the organization was bad.
On the other hand, I really liked the researchers I met with, and both campuses are beautiful. So MangoPlant, if you want to apply, you can, but I would keep your options open when applying (always good advice anyway, pick a lot of schools) because you might feel the same way.
Also, the stats OCDOCDOCD listed (the ones they give you at the interview) are for the med only program, I had emailed earlier about the MD/PhD stats since they aren't listed anywhere and was told they are 3.81/37.
http://imgur.com/PZ7wDUa
USC/Caltech lets you do your PhD at either institution with no questions asked, UCLA/Caltech has 2 spots specifically set aside for applicants that want to do the PhD at Caltech. It does seem to be an excessively long time and not so integrated at Caltech, but this is not true of all split school programs. I also interviewed at Indiana/Purdue and Wake Forest/Virginia Tech and they seemed to be very organized.