Currently, CPU wise there’s no reason to pick Intel over AMD performance wise. AMD’s got Intel beat on all fronts. Except maybe on availability 
11th gen might change this, but that’s still a while off.
The motherboards for AMD are also generally cheaper, and you can do all overclocking on all motherboards, don’t need special chipsets (or K versions of CPU’s) for that.
AMD/NVidia for GPU’s seems pretty much up in the air for MSFS right now, so pick whichever is available.
If you’re at all interested in the few current titles that support raytracing, NVidia is currently the clear winner.