A system of pay as you go "local" or commuting journeys combined with compulsory reservation intercity sounds great in theory but falls down in practice when you don't have a separation between short and long distance services or operator. Why should a less than one hour commute into London or Manchester for example on a season or PAYG be turn up and go but the same time and distance for a commute on the same ticket type now require reservations elsewhere in the country due to the lack of capacity of the operator concerned?
You'd also have the "Reading issue" - canny Reading commuters would reserve all the seats and nobody would be able to book a journey from Penzance. The only solution I could see for that would be season ticket holders only being able to pick up a seat on arrival at the station, but that would be awkward too. In essence as you say it only really works if your IC services don't carry a significant number of local passengers.
Clearly that will work for HS2 as it's effectively laid on top of the (slowed down) existing service, but it would certainly be an issue for XC and GWR, unless paths could be found for say a 4tph 12-car Reading-Slough-Paddington service to take all the commuters and ban them entirely from the 80x.