"There is no greater obstacle to knowledge than a formal education"
Mark Twain
An interesting historical insight....
Many of our gedolim didn't learn in yeshivos!! A list off the top of my head: Rav Elyashiv, Rav Soloveitchik, Lubavitcher Rebbe, Sfas Emes, Rav Yitzchak Isaac Herzog, Chazon Ish and many others. One then asks - Did they become great DESPITE the fact that they didn't learn in Yeshiva or DUE to the fact that they didn't learn in Yeshiva? Rabbi Berel Wein suggests that the latter is the case. A formal structured, educational system often stifles great minds. These people became so great because they were allowed the freedom to "roam" in Torah with being bound to a specific system of learning. I don't claim to have a great mind [partially because I don't:-)] but I can say that even though I was in Yeshiva for many, many years just about everything I learned was done outside the framework of the Yeshiva structure.
Practically speaking, this doesn't mean that we should close our Yeshivos. On the contrary, we should support the ones that exist and strengthen them. But it means that within our system we should try to allow all types of students to thrive and if a student needs more freedom it should be granted.