I don't think we need better cert agencies, I think we need a better system.
How I would set it up:
Every instructor would be independant from the actual cert agency. They could either be employed by a dive shop and get a salary or they could be fully independant and have a "school" similar to a driving school where they would teach everything from basic swimming all the way through scuba and specialties beyond.
You pick an aquatic school based on merit, advertising, word of mouth, referral from a dive shop, whatever.
Pay your money and go through the school.
The cert agency:
...Would be an entity (similar to DMV) where you are expected to know the skills of before you go in to take the written exam and diving (driving) test.
You make an appointment.
You go in, pay your money, and take the written exam, swimming test and other swim skills, do all your pool tests.
Set up for the open water dives however many required (irrelevant at this point). You would have to pass all the prior test to be eligible to take the open water exam.
There would be two or more open water endorsments, cold ocean , warm ocean, inland fresh, rough water management, etc.
You would automatically be endorsed for the conditions in which you took your open water. If for example you did your open water in a quarry and decided you wanted to go to Monterey and go kelp diving then you would have to do a checkout dive by someone certified to give you the endorsment (they would need to make sure you understand buoyancy and added task loading in heavy wetsuit, drysuit, etc.) The class portion of the added endorsment (if any) could be given prior by any instructor who teaches it.
If you were endorsed to dive cold water and wanted to go to warm there would be no reason for any added endorsment since warm water is ten times easier to dive in than cold. There could be other endorsments such as altitude, deep, etc just like specialties now.
If you failed at any of these skills in the testing faze then you would have to go back to your instructor and get in straightened out since the instructor is the one who was responsible for your training and skills building.
By keeping the instructors and cert agency separate, it would create an autoamtic check and balance system. As it is right now there would be a lot of instructors out of business.
It would be in the best interest of the instructor to make sure students know the skills and are proficient BEFORE they go get tested.
And the cool part. If you wanted, you could get a book and teach yourself to swim, skin dive, scuba dive, all the skills, etc.
As long as you pass all the skills at the cert office you are good to go.
The cert office would have everything on site, pool for swimming and deep end for scuba skills, class rooms, etc. It would be funded by testing fees.
It would also follow the standard set by the RSTC., or maybe a new one if the RSTC is too obsolete and crusty.
And yes, this system would cost more than scuba costs now.