The infrastructure has been improved through various electrification works, line upgrade schemes and extra platforms at Manchester Airport. There will still be failures of the infrastructure, but I’ve not seen any evidence that shows incidents have gone up markedly, only that the impact has due to the increased number of trains.The other factor to consider is that with the May 18 TT recast, there was a heck of a lot of capacity deemed to be “surplus” that NR/DfT thought needed using up. Turns out that cramming extra trains in doesn’t work without seismic infrastructure improvements.
This makes it a train planning and not an infrastructure issue; the infrastructure itself isn't causing the increase in unreliability. The previous instance of particularly poor performance was in May 2014, that followed the introduction of 5 fast trains an hour (a plan designed by First / Keolis TransPennine).
The routeing of trains through Manchester was based on the Northern Hub train plan, designed by the TOCs alongside NR and DfT, who all take some responsibility. First wanted to implement the May 2018 timetable, there were almost no changes from their advertised bid plan, and there was no suggestion from them that the timetable wouldn’t work: in fact TPE were still saying the timetable change would improve performance in their Summer 2018 customer report (see 'Transformational Timetables' page here http://www.liverpoolchamber.org.uk/UserFiles/file/Customer Report Summer 2018.pdf).
In addition, the extra frequency on the East Coast from May 2018 and the congestion caused by the joining of the stoppers were First’s ideas and weren’t mandated by the ITT (i.e. not caused by DfT or NR). See here for more info on the franchise ITT https://www.gov.uk/government/publications/transpennine-express-franchise-2015-invitation-to-tender
As for staff and fleet issues, they are the responsibility of the operator to plan and mitigate against.
The staff on the ground that I see all do a great job in very trying circumstances, and none of the criticism I see is aimed towards them. Those actually working on the railway see the issues and call them out. Unfortunately, they have to deal with the timetable plans and management initiatives given by head office, which for TPE have led to declining performance and the lowest level of passenger satisfaction since the start of what is now TransPennine Express.