I remember a conversation where an aikido instructor said his dojos teachers shouldn't be questioned because "I'm a Shihan [self appointed] and nobody tells me what to do"
In contrast, the general consensus within many "associated dojos" is you never question a shihan because well, he's a shihan - nothing need be stated, it's just understood...
I'm uneasy the implications that independent dojos occur through some lack of integrity on the part of the those who went independent. There are many reasons for leaving an association (or even being asked to leave) as some of the more "headline" dissociation's have shown. Note, I'm not saying the comment wasn't valid in some cases, but I don't believe it's the endemic reason. As for "complete freedom", believe me, it's a pain in the neck rather than a blessing and most independents in the UK normally adopt someone else's framework (often their parent association) rather than trying to build from the ground up.
The worry about stagnation is a valid one. However, I've met the odd non-independent dojo which has been even more insular than I thought was possible while remaining within an organization. So I'd put this down as more of an potential problem for all dojos, especially as most seminars are normally more open about heathens attending than in the past.