My impression is that MO yeshivas are more professional and better run. I also think they charge a lot more. Perhaps because the MO community tends to have fewer children per family, their total tuition bill is still manageable.
Chssidisher yeshivos I think are often really cheap. Because the community funds are used to run the school, shul, etc. So when they fund raise, the yeshiva gets its share. Although in tight times their girls school often gets the short end of the stick.
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My pet peeve on school funds:
Schools are often top heavy with administrators and staff getting salaries for doing very little.
There's too much nepotism in hiring for the top posts. Just because someone's father/grandfather/uncle was a good principal is not a reason to hire him to be principal straight out of kollel with no experience or formal training. So we end up hiring 2 people to do the job of the good, strong principal who retired.
(Adding to the problem of actually being mechanech the children: Teachers don't easily get fired for incompetence. If a new teacher needs more training and guidance, he should be allowed room to grow. But one who show incompetence year after year, needs a new profession. If a teacher has a mean streak he belongs out immediately.)
