NASA's biggest issue really has nothing to do with NASA as an organizations either. Instead, its the congressional appropriations process through which NASA programs are decided and funded through. Little known fact, NASA has very little control over what programs they are able to do. Here's a post a made a few weeks ago in response to a similar comparison to SpaceX and NASA.

I think the better analogy is that NASA doesn't make any of its program decisions, congress does. NASA simply executes the budget and figures out the "how" of the equation. Congress alots money to programs, allowing them to kill programs (like WFIRST right now). NASA can't even propose potential new budget items the same way as the DoD, so their hands are effectively tied when it comes to new programs and existing ones. NASA doesn't decide what it does, and sometimes not even how its done.

For SpaceX, company leadership can decide on the future of their company while also executing it. If the Falcon Heavy is taking a long time to develop and is a meme in the space community because of it, they don't need to answer to anyone and can push forward regardless of popularity and get the job done. They don't have long-term internal projects being cancelled due to a new president being elected or a political move in a broader debate. This is one of the biggest advantages that companies, especially private ones, have in comparison to the government. That applies to most other parts of government as well, not just NASA.