Small independents are no guarantee of quality either.I've seen some rather glaring quality control and performance issues with Tae Kwon Do comparatively speaking. It's definitely buyer beware out there. I've met TKD and TSD people that were phenomenal and I've walked into places and turned right around and walked out again. Massive orgs don't guarantee quality. You would think some level of oversight would take place but in my experience it's just not.
The thing people don't understand with large organizations is that their main purpose is to facilitate things that small independents usually can't. National and international events require large organizations, particularly large sporting events. The WTF, FIE (fencing), and FIK (kendo) are all examples of this, and each has national and local affiliates that feed into the international structure (USAT, USFA, and AUSKF being the United States national governing body for each of these sports/arts). Without competition, there's almost no need for such organizations, though they do exist for arts that don't have that element.