That is honestly a real bummer in the immersion department. The ultimate reason I want to do it this way is because I want to at some point make a persistent save. Where I load into where I left off then punch in my plan and file through ATC. I can deal with the requests up to my desired cruise but the arrival is often a total disaster if I follow given clearance.
So I guess my next area to explore is a payware ATC or just give up on ATC all together which is a real bummer.