Right, on its face this is simply more of the "drain the swamp" rhetoric from his first term. The way the EO is written sounds "fine" to my high school civics ears: there's three branches of government, one is the executive branch, and ostensibly the president is the head of that branch.
The motivation of the EO was clearly articulated all throughout the campaign that, as you say, even within the executive branch there's a large swath of career bureaucrats who kind of do their own thing. And so if the people vote for something else, there's kind of a limit to what any new administration can actually accomplish. Arguably, this is by design and provides valuable stability, but I think you have to at least acknowledge that it's there, and people aren't crazy for noticing it and trying to change that if the career bureaucrats aren't actually on their side.
I thought Trump was laughably ineffective his first time around. I chalked it up to all the Russia Manchurian Candidate stuff and Trump's constant flailing and hiring and firing of staff. But I'm wondering now how much of it really was this large bureaucracy in the executive branch not really moving in step with the new administration, which is interesting to me. I think there was a JD Vance interview (maybe with Ross Douthat in NYTimes?) where he says people throw around "constitutional crisis" a lot, but that he felt we were already in one because Trump was asking the generals stuff about troops in Afghanistan and they weren't answering.
I know people here are primed to read the worst into everything, and there's some seriously apocalyptic predictions in this discussion. But my first impression is that the EO reads fairly mundanely and is meant to sound like it's addressing the "hostile bureaucracy" situation that folks on the right have been talking about for years. I guess we'll see in a couple years, how it all plays out. I wish people predicted stuff more and then looked back to calibrate themselves based on the results.