Re: What exactly is an independent dojo?
I think it again depends on the dojo and the organization. What are the instructor's verifiable qualifications? Does the instructor have a Teacher? How often does the instructor visit/train with his or her teacher? What are the verifiable qualifications of his/her Teacher? When the instructor teaches, does he or she train with the students or just demo? What are the standards for rank? Is the aikido trained as budo, moving zen, aerobics, etc.? Are you paying testing/association fees? If yes, where does this money go?
As to the issue of stagnation, I think that's always going to be an issue when the head Teacher is of middling skill -- which I'm sure plenty can point to inside and outside of the main organizations -- AND has an investment in keeping the students dependent on him or her for advancement/knowledge/etc. (doesn't have to be financial, can be purely for ego). Which I think comes back to this: Is your teacher always trying to improve? Are they afraid to fail along the way? Assuming you do your work on and off the mat, are they trying to bring you up to their level (and hope that you someday surpass them)?