To be honest, I would take the Gareth Dennis position on nationalisation, which is that a slower transition is probably good, just to avoid unnecessary disruption for the most part.
In terms of your points on regional control, I would really disagree with the sentiment. A lot of politicians for the big city regions or nations are generally more pragmatic than you think. Northern cities tend to support infrastructure investments in other areas, because they see the knock on effects of delayed intercity services due to various bottlenecks. (E.g. Leeds sees delayed TPE train from Liverpool because of bottleneck in Manchester)
Devolution doesn't mean that regions can do whatever they want, and any kind of deal can ensure through ticketing and access for IC and freight services.
The issue is, the current system has a lot of people who are very out of touch signing off on the final decisions. Regional control seems to help rebalance that. Ridership numbers on Merseyrail, London Overground seem to confirm this!
Labour Party northern mayors are happy to ask for investment when they can say "Tories this, Tories that". Labour mayors under a Labour government would toe the party line which would involve not upsetting the electorate in other Labour heartlands. But either way they are responsible to their voters. A mayor of Greater Manchester isn't going to get any more votes by suggesting infrastructure improvements at Barrow in Furness to help the Airport to Barrow trains. A mayor of Greater Manchester
would get more votes by getting the Airport to Barrow train turned around at Bolton (or taken out of the path altogether) so he could say "we've increased seats on Bolton to the Airport by 'x'%". And your Merseyrail and London Overground services point is an example of what I'm saying. These are self-contained systems that largely don't go beyond the boundaries of their area (Chester and Orsmkirk aside).
I'm not sure a Greater Manchester Bee Rail, a West Yorkshire overground, a South Yorkshire Metro Rail, etc., is going to be helpful. Especially if it share the infrastructure with out of area services, but the prioritisation, control, and maintenance is run by, as part of, and for the benefit, of the local service.