Therefore what comes in its place post HS2? Will it still all be Macclesfield/Wilmslow-Stockport-Piccadilly or will intermediate stations get a look-in, therefore providing a more frequent service pattern and seeking to attract people out of their cars?
The short answer is we don't know. The best use will be made of the capacity at the time, which as it's well over a decade away (for Phase 2b) might be very different from what it is now.
To speculate on the examples you give, Macclesfield and Stoke are planned have a HS2 service to London so any remaining London trains on the classic route might pick up a few extra stops further south. There may be scope for extra stops at such as Kidsgrove, but there is still a need to provide Stoke and Macclesfield with fast trains to Manchester and Birmingham so a balance must be struck between these two objectives.