I really don't understand why Shanahan wouldn't just take over the GM reins himself, particularly since it appears he blocked some pretty substantial moves. Or do the due diligence, get your "guy" and let them mold their team into their vision. Otherwise we will always have this mismatch, messy neither here-nor-there rosters that aren't ever going to amount to anything.
I don't think it is as cut and dried as that. When the Shanahan/Dubas tandem started, they worked together as a pretty good team. We never heard anything about deals that fell through, because they were probably both on the same page. However, as the failures in the playoffs started to mount, Shanahan probably felt it prudent to go one direction and Dubas probably wanted to go in another. As those directions diverged, the partnership started to fail. Dubas couldn't convince Shanahan of why his direction was needed, and Shanahan couldn't impart on Dubas why his idea of how to build the team was the right idea. That's when the disjointedness comes in. I imagine, when it all started, Dubas had sold Shanahan on this idea that they would be high skilled hockey team, albeit on the smaller side. They would outskill and outskate the opposition. When that didn't bear fruit in the playoffs, Shanahan started to call the shots a little more, and that started to rankle Dubas a little bit, because he probably felt like he didn't have a voice or a role in the organization. When that happens though, it means that the only way for Dubas to stay is to eliminate Shanahan's voice and role in the organization. I can see how that would create a divide in the organization.
The media frames it as autonomy, but really, nobody has full autonomy. I'm sure owners of companies would love to do lots of things that would make them billions, but those dastardly politicians, and the tricky predicament of how not to piss off customers always comes into play.
In this case, I think when people say that Dubas wanted more autonomy, what we are really talking about is that he wanted direct access to the board, which meant that he didn't want to answer to Shanahan. Probably because he felt that either Shanahan wasn't actually telling the board what he wanted to do, or that Shanahan was explaining it wrong.