ywcomment2 pointed out one elephant in the room – rebbeim generally receive very little training. Their counterparts in girls’ schools, by contrast, often spend years studying to improve their teaching skills before they start. Should we be surprised that in general they are more effective?
Here’s another elephant. Many people who eventually become rebbeim have little education or training for any job (forget teaching), leaving them almost forced into becoming rebbeim. Imagine you can’t support your family on a kollel stipend, and aren’t qualified to work as an accountant, lawyer, etc, then you might turn to teaching, even if you’re not cut out for it. If “the system” provided a more robust education generally that allowed people to later pursue honorable professions, then in addition to alleviating tremendous poverty in our communities, we might also mitigate the oversupply of under-qualified rebbeim.