There are certainly some messy aspects to UK Rail, but the current system was not nearly as bad as made out by some posters , and there are some very good arguments against further centralisation.
A lot of the problem as I see it has been the misalignment between Network Rail (running the tracks) and the train operating companies (TOCs).
Firstly, NR is a huge and bloated bureaucracy - it is incredibly slow moving, and many of the problems (e.g. lack of modern rolling stock) can be directly traced back to problems with NR signing off on new rolling stock (they have to authorise each type of rolling stock to be run on each line).
Second, there are definite problems with timetabling - the TOCs are told the timetables they have to run. Unfortunately, the people who designed the timetables haven't worked out that in some congested areas (eg the approaches to Waterloo station in London), there is no way on earth that the timetables and service frequency of movements in and out of the stations are actually going work.
Thirdly, NR's investment in new systems has been very patchy. It is worth noting that the Welsh Government removed control of the Central Valley lines (serving the valleys North of Cardiff) from NR, and took direct control themselves, because they were sick of decades of underinvestment from NR, which generally takes a very London-centric approach.
Going forwards, I'm hopeful that we will see NR effectively split up into regional entities aligned with the TOC regions, so we can get much better alignment between infrastructure and rolling stock / services in each region. This may also enable a more equitable distribution of funding for infrastructure, which would enable infrastructure and service improvements especially in the North.
Finally, commuter rail and long distance passenger volumes have grown vastly over the past 20 years, which is a good thing. What is needed is infrastructure investment (particularly in modern signalling systems - ETMS) to enable trains to run much more closely together, and enable a higher service density. However, I think it is unlikely that the government will be prepared to make this investment.