Maybe it's just me, but...
All the bureaucracy is an attempt to respond to the development of a ginormous organization serving an even more ginormous nation and world, with a lot of moving parts, any of which can create a failure. Removing controls will allow a lot of creativity and innovation, but a lot of it could also be called unleashing loose cannons and chasing rabbits down trails.
Perhaps it's just based on my recent experience in the training commands, but a lot of young officers don't show up motivated and idealistic about the new Navy they're going to create, they show up shy and quiet, not wanting to rock the boat, and bored with all the bureaucratic process, the purpose for which they don't understand, always hoping to get time for either doing the one awesome thing they're there for, or do any leisure activity that doesn't involve the busy work of peripheral operations. They don't get stifled, they get kept in place for fear of losing the opportunity to do that cool thing that they do, be it flying, or blowing stuff up, or whatever. Enlisted folks come in pretty similarly, being nearly the same age and of similar personality that chooses to serve and join the adventure. In any case, those who don't get the "whole picture" need to be managed, lest they destroy the mission or their ability to take part in it.
Leadership is definitely needed, but not to start building an agile, optimizing, paradigm-shifting, buzzword-bingo-winning organization from the ground up. What is needed is vision and communication. Sobering. Honest. Apolitical. Inclusive, inspiring, and fair. And leadership mustn't always start from the top. We should each ask not what our country can do for us, but what we can do for our country. I could show up and be a really good stick, and be a pretty good GSO, and nobody else would be too sympathetic if I didn't get that awesome tour that will guarantee me a path to being a CAG and beyond, just because I think I have ideas.
One of the best leadership traits, one that is not often focused upon, is humility. The Peter Principle will hit everyone someday, and without humility, without knowing one's role in the grand scheme, it will hurt really bad and lead to the disgust that this article describes. Certainly some get the shaft, not all who are humble get their just dues, and not all who enjoy wild success are unhumble, but each one can always benefit from a humble, objective view of their world. I just can't help thinking that each of those creative JO's described who gets disgusted at the lack of opportunity and gets out, just gave up on some future chance at opportunity. Why else would it seem that there are only "average" candidates available for leadership? Taking opportunity for personal enrichment when it arrives is great, but if the goal is enriching the organization, then one should hang in until their turn comes. One cannot have his personal cake and eat Big Navy's cake, too.
There are a lot of facets to this, and I agree with or understand a lot of the sentiments of hope for improvement or dissatisfaction at its absence. But accusing the "system" and all the lazy, average, marginal leaders who seem to get all the top jobs of being the only problem is a little short-sighted. I'd like to see a few more articles about "what are YOU doing to improve YOUR Navy?" to go with all the ones about what's wrong.