To the OP: What is it you want from further training? If you decide that, then go and find an instructor and curriculum that provides it.
All classes (with perhaps some extremely rare exceptions) are run with an eye to profit and loss. Dive shops exist to make a profit, regardless of the agency with which they associate. Instructors, if full-time, need to make money, and even in our local model, where most instructors have day jobs and teach because they like to, they don't intend to LOSE money doing it. Dive shops CAN put significant pressure on instructors to cut costs -- cut pool time, use older equipment, accept higher ratios, etc. But dive shops can also have economies of scale -- I know when we teach private classes, the costs are high in part because we have to pay "retail" for our pool time, whereas the shop has a standing contract with the pool, and can spread the pool costs over multiple students and sometimes multiple class activities taking place concurrently.
Decide what you want from your training, and then ask questions of whatever instructional facility or instructor you are considering, to see if you will get it. The majority of agencies offering recreational diving classes are more similar than different. If you want to take classes from a nonprofit, look into GUE classes -- they are offered in Egypt! You will get excellent instruction, but you will pay a lot for it.
