Escalating supplemental application fees would limit applications to all schools, not just the new schools or schools with, how shall we say this, "quality control problems". Let's stay in Southern California, shall we? (The weather is nice). A 3.85, 90th percentile biology grad from UCLA wants to go to pharmacy school, and has four sorta-local schools to choose from: USC, UCSD, Loma Linda, and Western. (AUHS is on hold for a while.) Previously, this applicant would have thrown an application to all four of these schools, plus UCSF and Pacific as well. Six applications.
If the supplemental application fees climb to $500/pop as a weed-out mechanism (PatientLover's point aside that the max a CA school can keep appears to be $250/student- you'd still have to shell it out to apply)...how many supplemental apps is this student going to submit now? Probably two: one top choice plus one safety (need to make sure he/she gets in somewhere). Where the highly competitive schools USC, UCSD, and UCSF would have each gotten an application from this individual, now the applicant is just going to pick one of them and hope for the best.
As applicants become more choosy in their applications, all the schools are going to see a drop in applications. Let's suppose our applicant applies to USC and Western* and gets an interview at both. USC passes on the applicant, and Western accepts them- the applicant is going to Western. If the applicant had applied to all six schools, he/she might have gotten in to UCSD or UCSF.
This is going to cut both ways, but the sum game is this: students (especially the highly qualified ones) will become more choosy in their applications, and as such it will become more likely that students who apply to a school are going to go to that school if accepted. In the right market, a safety school may end up benefiting from this.
*I mean no disrespect to Western. I am not in the California market, and know nothing about this program.