Re: What exactly is an independent dojo?
I think it again depends on what you're looking for. I've heard so many times, "How high a rank can I get at your dojo?" or "What does it take to get a black belt?" from people that joined our independent dojo -- then didn't make it through a month of classes.
For the seasoned student, it's much easier to look at where the instructors (independent or otherwise) got their stuff, feel them on the mat (though it helps if you train at a place where the instructor trains with you, rather than walking around saying "do this, do that") and make an informed decision than it is for the brand new martial arts student that:
1) Doesn't understand the pros and cons that exist vis a vis belonging to an organization and being independent.
2) Doesn't have a basis for comparing the practitioners' skills (a compliant demo where people are flying through the air might seem more impressive than a less compliant demo where folks are dropped quickly and with minimal force).
3) Doesn't understand the difference between training aikido as martial art that you can fight with versus aikido training as learning to harmonize with the spirit of the universe (insert your own definitions of these things as it seems to be a case by case interpretation).
I train at an independent dojo and very much like it that way -- but I think that has more to do with my instructors, training partners and my perception of the quality of training than it does regarding the dojo's status as independent or otherwise (though, given my somewhat 'maverick' nature, I'm betting that it still IS a factor).