I have complained to Network Rail directly, although I do understand the points you make regarding who my contract was with (Northern). For me the compensation/delay repay is less relevant. We had a seat all the way from Manchester to Central Liverpool (via Headbolt Lane). We did not go for any specific return train and knew we would have to queue for some time. By then walking to Edge Hill we got home earlier than staying at Lime Street and we got a seat also! We arrived back in Manchester at 9pm when most others were still outside Lime Street. I consider myself to be a lucky one.
For me accountability and lessons learnt are the most important. I will be pushing Network Rail for better answers because I suspect the ones I receive will not be good enough. I want to see the Network Rail Managers from Lime Street being grilled in Westminster by a Transport Select Commitee so that they realise just how serious and abysmal their failure was. I am drafting a letter to my MP as has been recommened upthread, we should all do it.
Then if necessary I will make a Freedom of Information request to see what their future plans are for when Liverpool win the league next season as well

!
This is worth more to me than £9.45 I could probably claim for.