A consequence of centralizing governance in a giant federal bureaucracy is that it’s become dominated by one party: https://www.govexec.com/pay-benefits/2016/10/federal-employe.... That was a predictable result of federalization. If the government is run by unelected bureaucrats insulated from the elected officials, then it’s completely unsurprising it will become dominated by the party that prefers bigger government.
In classic Trump fashion, he doesn’t care about federalism per se, hence his inconsistent actions on law enforcement and crime. But he has a brain stem level reaction that it’s crazy he got elected President and is expected to cajole a federal workforce of 1.8 million democrats into executing his policies. And he’s not wrong about that.
Regarding the DOJ, Thomas Jefferson personally directed the prosecution of Aaron Burr: https://constitutioncenter.org/blog/the-great-trial-that-tes.... So that part isn’t anything new. As to the merits of the case, 18 USC 1001 is astonishingly (and I’d argue unconstitutionally) broad. I think prosecuting people for “obstruction” without an underlying crime is bullshit, but the government does it all the time. And Comey vociferously defended the practice.