The blame lies with everyone involved to be honest. The SWR network is at an all-time low, and the problems are caused by a myriad of parties. This is how I see it from a passenger point of view (obviously we are not fully informed, so don't jump on me if you take umbridge to any of this):
Problem: Frequent failures of signals, track circuit, etc. The cause of most delays and disruption on the line.
At fault: Network Rail. 100%.
Problem: Lack of contingency planning when things go wrong; still problems getting crew and trains to the right places.
At fault: SWR for not having plans in place, or effectively operating them. Also for killing staff morale, or not offering any incentives to mobilise staff, meaning staff are less likely to come in on days off to man trains when others are stuck (unlike other public services). And the union is at fault here too, for not allowing SWR to run trains without on-board crew for any length of time even though if a driver is there it is perfectly possible.
Problem: Regular faults on trains, leading to delays and disruption.
At fault: As far as I'm aware, SWR for skimping on maintenance of trains. Also the government for allowing such as woefully undercosted and unrealistic bid.
Problem: Regular congestion at peak times, leading to delays and disruption.
At fault: The government for imposing impossible timetable objectives on a creaking network.
Problem: Lack of communication to passengers, awful customer service.
At fault: SWR 100%.
Problem: Regular strikes.
At fault: SWR and RMT leadership being completely belligerant and non-compromising, with absolutely no interest in the paying passengers. The government can also take some blame here too.
All this adds to untold disruption for paying passengers, who are stuck in the middle of it all and pay an arm and a leg for a service with pitiful recompense (so far in January I've had over 10 hours cumulative delays on what should be a 45m commute, and I pay more than our mortgage payments for this). At least TPE had the decency to reverse the fare rises for this year for season ticket holders; SWR are at fault for this as well, and to an extent the government for not pressing them to recompense customers. The DFT seems completely useless right now in this instance. They seem more interested in pacifying their new northern voters than worrying about us down here.
This is my very long and cathartic answer to the posts above as to who is to blame for the problems on this line - mostly Network Rail, then SWR themselves and the government and, although I can't stand them, the RMT are a long way below these three.