I agree that DfT is equally culpable. They either knew this was going to happen and pushed the timetable change through anyway, which is bad, or didn't know and just assumed that GTR knew what they were doing, which is worse.
Don't forget; however, that DfT are only implementing government policy. That policy seems rooted in the dogma that the free-market is the solution to all problems. The free market should be nowhere near any aspect of national infrastructure, such as utilities, NHS, roads, waterways and railways. That's because the free market's only aim is to make as much profit as possible for as little outlay as possible. GTR's primary responsibility is to deliver value to its shareholders, which it is attempting to do by maximising profit from the management contract handed out by DfT on behalf of HM Govt. Tory dogma has driven the notion that somehow the rail industry should cover its costs through ticket revenue and that any funding from taxation is in some way bad. Yet the majority of the funding for roads in the UK comes from general taxation, plus a contribution from VED and a small amount from tolls. This is acceptable because the road infrastructure is considered a benefit to the nation as a whole.
The same principle ought to apply to the railway. The network was systematically starved of investment by successive governments of all political persuasions, who thought they knew how to run things on the cheap. We should have electrified immediately after WWII or continued with strategic pockets of steam operation through until electrification was completed in the mid 1980s. Instead we wasted millions on building steam locos that had working lives of ten years or less, followed by unreliable diesels that had similarly short lives. There has never been a unified strategic plan for the railway, just petty tinkering and piecemeal projects, which get cancelled or descaled when the next government takes power.
How much money is being wasted on HS2 just to reduce the London - Birmingham journey time by 20 mins? £90 billion, £100 billion, £150 billion? You could use that money to electrify the GWML and MML.
The railway and Thameslink in particular, has been offered to private enterprise to see whether they could make it work and the great experiment has shown that men (or women) in sharp suits are no better at running the railway than men in greasy overalls were. The only difference is that now the trains have less comfortable seats and get reliveried more frequently. Oh, and the other differenece is that somewhere along the line, the men (or women) in the sharp suits and their shareholders get to syphon off some of the money that ought to be recycled into the railway to make things better.
We should be taking the railways back into public ownership immediately and begging railway operations experts from across the world to come and show us how to run a railway properly, because we sure as hell seem to have forgotten how to do it.