Bearing in mind, McNulty himself found the railway in its present set-up to be less efficient than its European counterparts at the moment, I'm not convinced that what improvements in efficiency there may have been (I've not seen anything quantified as yet) are entirely down to the private TOC model.
That's as opposed to other technical advances which might have happened anyway (an example being the increased use of software etc which has transformed back office and clerical functions throughout industry over the last twenty years) and outsourcing etc.
McNulty found exactly what it was set up to find - quelle surprise! Not that I don't think efficiency can be improved. It can be improved significantly. But when it comes down to specific suggestions on improving efficiency McNulty is pretty thin on the ground.
My own recipe for improvement would be:
1. NR purchasing. Must be the biggest area for savings as it is the biggest cost. NR tend to go for gold-plated solutions and vanity projects. To be fair they have already made some improvements, but there is plenty of room for more.
2. Removal of arcane staff practices that lead to huge inefficiencies - the practical side of this however is a complete minefield, and I doubt that anyone has the intestinal fortitude to take it on.
3. Removing duplicate duties, red tape, etc. that lead to pointless posts & consultant fees at DfT, ORR, NR, and to a very minor extent at TOCs. This last is much smaller in scope than the other two in terms of savings, but it may help pave the way for number 1.
As for your second point, it's simply factually wrong:
1. The TOCs started in 1997, which is 15 years ago, not 20.
2. Many of the same systems that were in place then are still in place. For example SAP is still used by many TOCs including all the First ones, and what the others use is actually less advanced, not more.
3. Where systems have been updated, e.g. Lennon replacing Capri, they have often led to additional posts. This is a common misconception; more information needs more analysis. The pay back on Lennon is in increased revenue yields.
The savings that have been made are real savings. Current organisational structures are much flatter than under BR, with whole levels of management removed.
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Not all of it, part of it is from the fare box through the TOCs. If NR was not subsidized then it's likely that fares would have to be increased even more to cover this.
Yes, of course, NR get paid Track & Station Access from the TOCs, many of whom also receive direct subsidies from the government, but many who pay. Regardless, this is the same finance mechanism as under BR.