I'd be very surprised if diagramming, rostering and route knowledge weren't highlighted, not as the root cause of TPE's woes, but as the reason why their "behind the scenes" problems are transferred so completely and harshly onto passengers.
When you fragment routes into tiny parts, passing through stations where unplanned platform occupations would cause chaos, the caution you have to exercise in letting a train leave it's origin is so insanely high. It can be a challenge to get two train crew and a maintained train in the right place at the right time. TPE have set themselves up so that the planets need to align for anything more than a Huddersfield stopper to run. This is, from a frontline POV, a massive issue.
"Lack of train crew" is a genuine problem, but the real reason for so many cancellations, delays and problems is that, at TPE, it's more like "not enough train crew to run a service using the methods we doggedly cling to in pursuit of potential (but never achieved) efficiency and cost savings" - if running a train service was a video game, TPE have been playing on the hardest mode when they know they can barely get through the first level in one piece.
How much will be changed after the changeover, I'm not sure. But there's potential for these cultural problems to be identified and worked on. I know that at Northern the "first 100 days" led to some quite deep exploration of what was going wrong. I pray for the same for TPE.