I don't see how a brand new route built in recent years should somehow be 'made' to fit into this structure......your implication is that the industry needs to have more control from the regulatory authorities, but the current fares and ticketing mess can be traced directly to the completely half-baked inability of those authorities to actually let the industry manage this area properly.
The existing regulatory regime was a half-baked attempt to contractualise BR's 1980s fares structure which didn't work properly at the time, and definitely doesn't work in the second decade of the 21st century. A much simpler mechanism that specified a maximum fare between stations and let the industry sort the rest out would work much better.
Of course, it could be argued that both routes via High Wycombe and Reading were once part of the Great Western Railway and as Oxford/Kidlington Parkway is between both mainline routes, it does seem reasonable to attempt to fit it in so as the Any Permitted fare should be valid for either route.
Regarding the last sentence in the second paragraph, there have been some threads that had a discussion on suggestions to improve the fares system. I remember that there were various suggestions that included purely based on mileage (unworkable in my view due to various easements allowing doublebacks, stations such as Reddish South and Denton having a frequency of one train every seven days in one direction only etc), and also suggestions I believe from regular poster Neil Williams suggesting a base fare plus type of service such as local all stations service, regional service, and traditional Intercity service. I am not going to rehash recent arguments about this, and if I remember correctly, there was not an unanimous verdict either way that was reached or agreed upon.