Regarding the present parliamentary/limited service routes and stations, and in relation to the earlier DfT document, I have a few thoughts in my mind in how to improve the services.
1) The section of the Manchester, Sheffield, and Lincolnshire Railway between Sheffield Midland and Worksop/Retford is to have its frequency doubled from every 60 minutes to every 30 minutes by means of a short working. The Sheffield - Lincoln Central service to remain every 60 minutes at present, with a short working between Sheffield and Retford every 60 minutes. This would combine to give a frequency of every 30 minutes between Sheffield and Retford, also retimed slightly to give better connections from the Nottingham - Worksop service. The Sheffield - Retford service could be extended every 2 hours to Grimsby Town/Cleethorpes via Brigg as an experimental service.
2) The present Sheffield Midland - York via Pontefract Baghill to be improved to every 2 hours thoughout the day. This would provide Pontefract with improved access to the Intercity network on a north-south axis.
3) The proposed Manchester Victoria - Chester/Ellesmere Port service via Warrington Bank Quay to operate every 60 minutes between Manchester Victoria and Helsby, with one train every 2 hours continuing to Chester and one every 2 hours to Ellesmere Port. This would improve the frequency between Ellesmere Port and Warrington BQ/Manchester, and would have the potential of attracting some passengers at Ince & Elton as there appears to be a recentish residential development south of that station.
4) The Halton Curve when the works are completed to have a Liverpool Lime Street - Chester service every 60 minutes, with one train every 2 hours continuing to Holyhead, and one train every 2 hours continuing to Cardiff Central via Wrexham, Shrewsbury, and Hereford. Perhaps a partnership could be formed with the operaters of the Wales & Borders/Welsh Government in regards to developing such a service?
5) The present Leeds City - Knottingley service to be extended every 2 hours to Goole as an experimental service. This would greatly improve the present level of service it presently receives.
6) The famous Stockport - Stalybridge Fridays Only service to remain as a shuttle between those points for the time being, but to operate every 2 hours daily. In time, this could gradually be increased to every 60 minutes, and maybe operate as a local Stockport - Huddersfield all stations service. This would obviously have to have a good connection at Stalybridge for Manchester to and from the local stations between Huddersfield and Stalybridge, and may or may not reduce some of the congestion along the route.
By starting off with a 2 hourly service, this means that the service level could be increased from there, as was demonstrated on the Great Central Railway/Great Western Railway Alternative Route when Network SouthEast introduced the London Marylebone - Birmingham Snow Hill service back in 1993. That route now sees 2 trains every hour today after going from every 2 hours - every 60 minutes - 2 trains per hour.