TSandM pretty much covered it all, so I'll just point and nod...
Personally, I decided to be quasi-independent. I decided that I wanted my own insurance for various reasons, independence being one. On the other hand, when I'm in town, there's really only one shop that I am comfortable working with, so I'm de facto associated, at least locally. I work their classes and trips as often as I can, so I have much more opportunity than I would purely independent. It's enough of an association to the shop that I get the "key man" discounts and other benefits, but it's also independent enough that I'm not an indentured servant being paid in insurance and gear discounts. I *do* find it terribly convenient that they handle all the paperwork and logistics for me.
In order for it to work, we did have to (quite easily) come to an understanding about things like gear. I dive a jacket BC in the pool and spring-day on the checkouts, and then I dive my backplate on the saltwater days of the checkout. They don't sell the fins I wear, but they make it up in spring straps and beanie caps sold. To them, I match enough to not hinder instruction in the early stages, and they get to show me off on the boat as an example of other gear or other areas of diving. I get to dive my preferred gear in the water that matters, and the pool water only attacks my class gear. :biggrin:
If the shop were more like some of the hard-line shops I've read about, it might be more difficult to have a loose but mutually beneficial quasi-association. I'm not sure I'd want to associate with a shop that *doesn't* allow loose affiliations, on the other hand, so that would likely make the decision even easier (just like not-purchased-here syndrome makes it trivial for a customer to walk away from a shop with bad feelings).
I'm now an Instructor, still operating the same way I did when I made Divemaster, and it seems to work just as well now. Well, better, as mb finished her Divemaster, so we're a quasi-independent dynamic scuba duo. :biggrin: