I don't think that it is so much the pilot mills that's the problem as much as some of the people coming through them. I went through one of those "mills" to get my instrument through MEI. I however was a private pilot for quite a while prior and enjoyed flying alone or with my buddies and just being up in the air. I personally know that there is so much more to flying than what is taught in these big schools and I aim to keep on learning. The problem is that quite a few of these students come through and somehow believe that what they learned at this school is the end-all, be-all, of flying. The looks of shock on their face when I told some of them that yes, you can in fact land a c-172 in a 23 knot crosswind (that 15kts was max demonstrated and not a rule) or when I told them that yes, you CAN forward slip a C-172 with full flaps and they told me it was against the rules (I had to explain the difference between "avoid" and prohibited". One of them said that if this technique was done you would fall out of the sky and die.) is all kind of scary. Now I am not trying to sound like I know all about aviation because I do not, not by a long shot, but a lot of these schools are telling these students that these techniques are gospel, instead of simply ONE way of doing things.
These attitudes sound a lot like what some of you are saying you are running into in the cockpit.