I would suggest the following for franchise remapping, being as Scotrail has always existed since the days of British Rail:
Regional Railways North West - this would include the limited stop inter regional services, the present TPE Manchester Airport - Glasgow/Edinburgh via Preston, and local all stations services specified with input from Merseyside Passenger Transport Executive (PTE) and Greater Manchester Passenger Transport Executive.
Regional Railways North East - limited stop inter regional services and those operated by TPE via Leeds/Sheffield, the Liverpool - Norwich as far as Nottingham, Newcastle - Carlisle, and local all stations services specified with input from Tyne & Wear PTE, West Yorkshire PTE, and South Yorkshire PTE.
Regional Railways Central - limited stop inter regional services that are presently part of Crosscountry, Birmingham - Hereford via Bromsgrove, East Midlands local, and local all stations services in the West Midlands specified with input from West Midlands PTE.
Regional Railways Wales & West - limited stop inter regional services from Swansea or Cardiff to Manchester, Aberystwyth/Pwllheli - Birmingham, and the present GWR inter regional services. All local services within Wales to be specified by the local councils within each of the 8 preserved counties (if I am using the right terminology here, I refer to Gwynedd, Clwyd, Powys, Dyfed, West Glamorgan, Mid Glamorgan, South Glamorgan, and Gwent), with the Senedd having a bit of input into the Intercity and cross border inter regional services. Somerset, Wiltshire, Devon, and Cornwall also have input at county (or national for Cornish nationalists) level, with further input from local councils.
Network SouthEast - the divisions based on the the three former railway companies south of the mighty Thames: London & South Western, London, Brighton, & South Coast, and South Eastern. Gatwick Express brand to be abolished, and replaced with London Victoria - Brighton calling Clapham Junction, East Croydon, Haywards Heath, and Brighton. Ashford (Kent) - Hastings to transferred back to Southeastern, as the Southeastern Railway built the line in the first place. Local services within and to the first junction station outwith the London Travelcard Zones to transfer to TfL.
C2C - Leave as is, with maybe the transfer of Romford - Upminster from TfL Rail.
Great Eastern - leave as is, with maybe the transfer of the Nottingham - Norwich section of the present Liverpool - Norwich service.
Great Western - Traditional Intercity services, plus the Thames Branches, Great Malvern - Bristol, Newbury/Bedwyn, Swindon - Westbury/other destinations via Melksham, and some Oxford terminators extended to Banbury.
Chiltern - leave as is, with Aylesbury Vale Parkway trains extended to Milton Keynes and Bedford, and possible incorporation of the Birmingham Snow Hill locals.
Great Northern - Moorgate services transfer to TfL, with Kings Cross - Kings Lynn transferring to East Coast.
Thameslink - no trains to touch the former North Kent Railway metals at all. Bedford - Brighton limited stop to revert to a 15 minute frequency, with a train every 30 minutes calling at Redhill. Also, get the present mess sorted.
Home Counties Connect - New franchise which would include London Euston - Birmingham via Northampton, St Pancras - Corby, Bletchley - Bedford local. These would be the services of the former Network SouthEast north of the mighty Thames that have not been mentioned elsewhere, and those which will not be part of London Crossrail or have TfL input.
Intercity East Coast - the present Kings Cross - Edinburgh Waverley trains running non-stop between Kings Cross and York to omit Darlington Bank Top, and extended every 2 hours alternating between Glasgow Central via Motherwell, and Aberdeen via Kirkcaldy. The Crosscountry to revert to terminating at Edinburgh. Also, would incorporate the Kings Cross - Kings Lynn services.
Intercity Midland - one train every 2 hours extended from Sheffield Midland to Leeds calling Meadowhall Interchange (for HS2), Barnsley Interchange, Wakefield Kirkgate, and Leeds. The opposite hour every 2 hours to be extended to York calling Meadowhall Interchange (for HS2), Rotherham Masborough (re-opened), Pontefract Baghill, and York.
Intercity West Coast - the London Euston - Glasgow Central via Trent Valley Railway to have the calls reinstated at Watford Junction, Rugby, Crewe, and Motherwell that were cut at the December 2008 timetable change. The section of the Birmingham New Street - Glasgow/Edinburgh via Preston to be incorporated and revert back to Crosscountry. Liverpool trains to alternate calls between Nuneaton and Tamworth.
Intercity Crosscountry - transfer the inter regional limited stop routes to Regional Railways Central. The Birmingham - Glasgow/Edinburgh via Preston to be transferred back to Crosscountry. In partnership with South Yorkshire PTE, trains via Sheffield could call at a re-opened Rotherham Masborough. Basingstoke - Manchester/Nottingham/Sheffield via East West Rail to be operated by ICXC.
Knowing me, I have probably missed a few obvious ones, and have broadly (from memory) have based it on the regions and sectors of BR.