Lots of reasons on the Great Western. The main problem is pathing problems for late running, made worse by the single line sections on the Cotswold and Golden valley routes. Oxford and Reading stations are pretty much worked to capacity. Any sort of failure at these locations makes things very bad. There's about the same number of trains handled at Oxford as Sheffield, through 2 through platforms and a bay. Reading station handles more passengers than the whole of the NE of England put together.
Reading and Slough PSBs are getting unreliable and much of the trackwork, apart from the London area, is from the 60s or 70s. The HSTs are getting a bit tired now, and the maximum is made of the 165/6 turbos. It's still essentially the same railway as in the 60s/70s with the exception of the London area, which runs almost to capacity with the Heathrow services.
The Great Western main line is also a suicide hotspot, with Ealing Broadway and Southall being problem areas.
Low speed freight is difficult to path, especially Reading area, London area, Didcot-Banbury and Didcot-Swindon.
Further west the picture is better, but really it doesn't matter who runs it, it's a line that carries a lot more than it ever has, designed in the 60s/70s for an era of falling traffic. Any calls for nationalisation will do no good, it just needs a serious amount of money spending on it.
