The underlying issue with all public transport is that it is a revenue system, not a public service.
The service WILL NEVER EVER EVER get any better while in the hands of corporate organisations who only want to extract money from it.
Yes, the trains were founded by commercial investors looking to make a profit, but at that time, no alternative existed that could match them. Now, Road and Air compete, preventing the 'quick and dirty rail lines' from actually working.
In my opinion, the ONLY way things will get better is one of these two things happen
1 - The ENTIRE system is re-nationalised, and NO Contractors or Sub Contractors are used. (yes, that kills companies who only do rail contracting) The government then runs it as a public service, but income from the railways is NOT allowed to enter the public taxation pool, and thus most be invested back into the infrastructure, improving the system overall.
2 - The ENTIRE system is handed over to a non-governmental, non-profit company, to manage. The same applies as above. No profit, just money returned into the system.
This will allow more improvements to the infrastructure (HS2 for instance), the reduction of ticket prices, and the whole thing managed on a countrywide scale, improving efficiency.