I agree that “self certification of safety compliance” is the height of “cozy,” and borders on negligence of the oversight function. Both places (Boeing and the FAA) have been gutted of their engineering expertise because engineers are very, very expensive...especially those with the very specific expertise required...and the “what could go do wrong it could cost more than we are saving” business mentality that has blown up in their faces.
In general, I think the checks and balances were just fine. In this particular instance, you had Boeing designing a system to fix one of the Frankenstein problems that came from the “old type, new aircraft” problem. That system SHOULD have been made transparent and open, but Boeing feared it would require simulator training. SOUTHWEST AIRLINES has driven B737 development for years, as the world’s largest owner-operator, which is why the overhead panel is circa 1960 and so few “automatic” update options from newer aircraft are allowed into the aircraft. SWA wanted it to be a “no sim, minimal CBT time” aircraft. Boeing employees, seeking to allay customer fears, did that by hiding this brand new flight control system from airlines and giving it short shrift with regulators. In short, Boeing pilots and engineers lied about what it was and how powerful it might be.
I think THAT problem has been fixed to everyone’s satisfaction (no more single source input, other protections such as one time activation that can be overridden, new complete procedures, etc.) but the wider problem of that “cozy” relationship is a bigger issue.
Boeing has been pushing more and more output towards South Carolina and away from its tradition roots in the Seattle, WA area due to “more favorable business environment.” In short, non-union labor. Not many people (as in experienced engineers and fabricators with decades of expertise) have made that move. Accordingly, the first wave of 787s made down there are literally UNAIRWORTHY, and thus unflyable! Instead, they’re in museums and such.
THAT problem...loss of expertise and experience, coupled with a profit-driven imperative over the previous engineering excellence motivation, is a problem I’m not sure Boeing will ever overcome.