HaLeivi> I fully believe that the Yeshiva I send to (and went to) does not splurge on unnecessary things.
even then, running a big institution has overhead – building, secretary, ads, bunch of people on payroll that are doing something useful – fundraising, teaching a once-a-week class, fun trips … if you can organize a small class in a house and Jewishly-educated parents chip in with their skills a little and you hire teachers you prefer, you can do much better, both in costs and quality. This is not just my opinion, I heard this from a couple of talmidei chachomim who preferred to run their small operations without joining bigger mosdos.
One thing that may give you a pause – you will not be paying higher tuition for those parents who pay less, but 1. chayecha kodmim, 2. you can always pay tzedokah, for example, to those who are teaching in your school.