The only way forward is to scrap all this and adopt the old SNCF policy of x francs per km single journey, plus 50% for a return, add 50% for Ist Class and a discount for children and pensioners, and THAT IS IT. Everyone knows where they are and people will quickly learn the most crowded lines/trains and, with everyone paying the same amount as with petrol in cars government will know where to build new lines and companies will know when and where to put on more trains as all subsidies directly to them will end. Simplistic? - obviously, but a darned sight better than the increasingly ludicrous position we've got ourselves into now.
So will it cost a different amount from Bradford Forster Square to Leeds than from Bradford Interchange to Leeds? What if you're in Leeds and the next train in is to Interchange and you bought a ticket to Forster Square?
Simple?