Here is the thing...
When you learn a basic curriculum, sooner or later, if you are serious about yourself and your training, you are going to ask questions regarding two very related things: You are going to ask questions on what are the basics, what are they really; and you are going to ask questions on what is beyond the basics (which the word "basics" implies - that there is something beyond them). If you are of the nature and/or lifestyle where these questions are framed from within a martial paradigm, you are inevitably going to seek and do a type of training that is related to the development of basics, or the refinement of basics, in a martial sense but you are, unlike before you asked these kinds of questions, no longer going to settle upon training devices/drills that gave you the basics and the questions in the first place. There's going to be a departure of sorts - because there has to be.
Thus my comments on shu-ha-ri. What you're describing is what it feels like to be heading into a 'ha' phase of training. Rote mimicry becomes painful somehow to the practitioner as they start to reject some things that they had taken for granted. Suddenly they find themselves questioning all of the basics, looking for holes rather than for where they are valid. The danger here, is not being guided through this process. A greater danger is deciding to open a dojo at this point.
I agree that too many dojo cho are plodding along doing the exact same thing they have always done, repeating verbatim what they were taught decades ago. Frankly, a lot of people never get to the ha phase, they spend their entire martial careers in a vain attempt to mimic their teachers to a precision that is absurd. They often get very good at what they do, but they do not have the understanding that they would have gained if they had toughed it out through the ha phase, admitting to themselves and their teachers that they had doubts and working through them.
The presentation of shu-ha-ri is something I really admire Kendo for. To present this idea, that it's normal to doubt, get frustrated, even outright reject what one has been taught can go a long way in helping the student through that period. Of course, one can only be guided if one's teacher is up to the task, meaning that they have made that transition themselves. Many, unfortunately, have not.
For those of you less familiar with shu-ha-ri, please understand that I don't mean to imply that these phases are somehow are rigid, or that being in the ri phase of ones training amounts to enlightenment or anything so lofty. There is a nice article archived on the aikido FAQ here.
Note that in the article, they refer to the 'lonely' student. It is fairly common due to the relatively rare nature of Iai instruction (the author's context) for students to continue training on their own or in study groups that only get infrequent correction/face time with their supervising instructors. It should not be confused with someone who has broken off on their own against the teaching of the ryu-ha. The goal of the student is still to progress within the context of their ryu-ha.