Some have said about grouping with the IC operator, but which one for example would Newcastle - Carlisle be east coast or West Coast etc.
Newcastle to Carlisle would be with East Coast as the units for that service are allocated to and maintained at Heaton. It would be no different to the Regional Railways North East/North West arrangement.
I believe that Transpennine Express should be kept as a separate entity, as it works well being treated as a long distance regional operator rather than as an annexe of a local train operators activities, but only for as long as the franchise boundaries are maintained as they are. Except for the Manchester to Scotland route, which should be incorporated into the West Coast franchise as a top priority.
However, were electrification of Transpennine North to be on the cards, then in the run up to such a scheme I would hand over Manchester Airport to Cleethorpes to EMT, and incorporate Transpennine North into the Northern franchise. EMT would gain additional 158s, either from ATW or Scotrail through an arrangement of cascades, to operate the Manchester to Cleethorpes service.
IMO Northern works very well as a combined single entity, and the only resplit of the franchise I would support would be if there was an aggressive redefining of the franchise boundaries to reduce the number of separate franchises, which would see the North West local services incorporated into the West Coast franchise and the North East local services incorporated into the East Coast franchise.
The franchises would then be arranged thus: Scotrail, West Coast, East Coast, East Midlands/MML, Crosscountry, Wales, Great Western (absorbing Chiltern), Anglia, London Overground, Crossrail (Could be part of the Anglia franchise, or joint operated by Anglia/Great Western), Thameslink (Could be part of the Southern franchise) and the three Southern region third rail TOCs. Of course, in this model TPE would logically have to either remain as a separate entity or be combined into the XC franchise.
Strategic electrification schemes around Britain would allow all of Northerns' Pacers to be replaced by cascaded Sprinters or directly by EMUs, so new rolling stock wouldn't be required until the replacement of the Sprinter classes occured. The electrification schemes required to do this would be Cardiff Valleys, Transpennine North, Uckfield & Marshlink and all of the Scottish Central Belt, extended north to cover Perth/Dundee to Aberdeen. MML electrification would be useful as well to allow the majority of the West & South Yorkshire local services to go over to electric operation through a combination of branches of that scheme and the Transpennine scheme.
New diesel rolling stock to replace the Sprinters on the remaining unelectrified routes when that time comes would be in the form of whatever the 2025-2030 equivalent of the class 172 is.