Personal comments: the inaccurate routing and “phantom USR waypoints” have been long present in the flight planning and routing logic.
Presumably this is one of the many items to be addressed by Sim Updates 4 through 6 as noted on the Feedback Snapshot.
How to mitigate (but not fully); use an external tool like an EFB and import your plan. I use Little Nav Map, many people like Simbrief. Secondly, get better NavData. NavBlue has many shortcomings. An annual Navigraph data only subscription gets me very accurate data on current AIRAC. Between that and LNM, I have complete graphical views of all SID/STAR and approaches, as well as good routing across airways.
For the most part, about 8/10 plans cleanly import into the sim using this method, meaning no massive curves, no insertion of Phantom Waypoints etc.
Departures are usually straightforward and WYSIWYG. Approaches, well, approaches are what make life interesting in this sim, and that’s before you even get to the Initial Fix.