Again, I'm late to comment. My school belongs to GM Shin's WTSDA. I live in a small town now, and there are only - I think - two martial arts schools in town that have national or international affiliations. The rest are independent. Before moving here, I trained in Shotokan at a JKA affiliate school. To me, I would never belong to a school that did not have some fairly mainstream organizational ties.
Here's why:
Some even and widespread standards for promotion. Hopefully, no ranks for sale, if you know what I mean.
Students can take their rank and go other places. Even if there is no local school where they land, most of the larger and more reputable organizations will meet you half-way if you have a rank from another genuine group. But a ranking from an independent school often is meaningless.
Opportunity to train with high-ranking teachers, often from the old country.
Large, national events, with consistent judging and rules.
Less of a tendency for the teacher's bad habits and idiosyncrasies - we all have them - from becoming incorporated into the syllabus, because the teacher and the school are not isolated.
I could go on, but that covers most of it. Not trying to put down independent schools, but we should admit that some independent schools lack standards, and give a bad name to the others. I am especially cautious about the local guy who says, in effect, "I took the best from shotokan, aikido, judo and TKD, and created my own style." Such a fellow is rating his own ability ahead of styles and groups with many years of experience and many great practitioners.
We pay a relatively small fee to the parent organization, for registrations, ranks, events and the like. It's a good trade-off to me. The students benefit most of all.