It depends on the aircraft, the stock ones and things like the FBW A320 allow you to just set the FMS and then request clearance from that. Others that did their own navdata like the CRJ or PMDG 737 unfortunately need ‘both ends’ updated with the same plan. What I do is plan it all out in Simbrief and then export (using the automatic 'Simbrief downloader app, from the simbrief site) a local aircraft file (say, for the PMDG) plus the MSFS2020 .pln file - then I load that in the world map and then load up the FMS simbrief plan. That way all the ATC matches up. One other ‘funny’ in this is that by default you won’t start at a gate importing a .pln file, so once it’s loaded use the dropdown list on the World Map to pick a gate (there is a bug if you select a ‘dot’ on the map it alters the plan, just use the dropdown and it’ll keep it unchanged).
For the Change Runway, it’s a little odd in that Clearance will assign you what it feels is the active runway (according to just wind) but then you need to get to the ‘Request IFR Taxi’ step with the Ground controller. At that point you can request a better runway, although it doesn’t let you go against the wind (which is not good and might be what you want). Here’s an example where I request a different (and closer) runway:
They do still have a heap to do still on ATC for sure, but I think it’s going to take a while. Starting with the FSX base probably didn’t do them any favors on retrospect. Good ATC is one of those things that is a lot more complicated that it would seem at first.