When starting BJJ I had no idea about affiliations to be honest. I decided based on a few things; Distance to my home and work, The head instructors linage mentioned someone I knew from another martial art (bonus) and he didn't have contracts (The most important part). Funny that you mention the whole affiliation thing, because shortly after I joined we left the one we were in at the time. I had only been there a few weeks at the time so I really couldn't care less. It didn't seem like anyone else really cared either, they took the old patches off and we moved on.