I agree that an intercity operator should handle this differently than local trains. I've lost count of people bleating on about 'intercity ambience', a standing persons elbow in the ear ruins ambience rather more more than 1/3, 2/3 door positions IMO.
What exactly is an inter-city service though? (genuine question)
Euston - Milton Keynes with Virgin?
Paddington - Reading with GWR?
Both operated by what we'd all consider to be inter-city trains but crowded with commuters at certain times of the day. If you banned the standing commuters by making it compulsory reservations then what trains would they travel on? The other trains between Paddington and Reading/Milton Keynes are wedged at peak times. There is no capacity to run additional trains.
The problem is that our inter-city trains are also used for short distance journeys as well. This isn't unique to Milton Keynes and Reading. There are loads of similar instances across the country. That is the problem and I don't really know how you can balance everything.
n my view the status-quo is probably the least worst option.