I have created an entire set of timetables (Mon-Sat) for every railway line in the UK. Yes, it did take me 3 years. Yes, I am constantly changing it. The biggest differences with the current timetables are:
Thameslink:
Cambridge-Tunbridge Wells (2tph, slow then semi-fast)
Tunbridge Wells-Bedford (2tph, semi fast)
Bedford-Horsham (2tph, semi-fast)
Horsham-Cambridge (2tph, semi-fast then slow)
Peterborough-Hastings via Gatwick Airport (2tph)
Brighton-Kings Lynn (2tph, express)
Caterham-Stevenage (2tph, stopping)
SouthEastern:
Charing Cross to Rainham: Waterloo East, London Bridge, New Eltham, Sidcup, Dartford, Greenhithe, Gravesend then all stations
6tph Fast Charing Cross to Kent (2tph Hastings, 2tph Canterbury West, 2tph Dover with various extensions onwards to Ramsgate)
7tph HighSpeed (2tph Faversham & Margate, 2tph Canterbury West & Margate, 2tph Dover & Ramsgate, 1tph Maidstone)
Charing Cross to Maidstone: Waterloo East, London Bridge, Grove Park, Swanley, Maidstone East
Northern:
Manchester to Lincoln: Stockport, Hazel Grove, Chinley, Dore & Totley, Sheffield, Worksop, Retford, Gainsborough Lea Road, Lincoln
Manchester to Blackpool: Heald Green, Manchester Piccadilly, Manchester Oxford Road, Salford Crescent, Bolton, Preston, Poulton-le-Fylde, Blackpool North
Manchester to Wigan: Salford Central, Salford Crescent, Hindley, Wigan North Western
Leeds to Carlisle runs hourly, alternating between all stations via the Settle-Carlisle line and calling only at Settle and Appleby
Manchester to Millom (semi-fast)
Re-introcude the fast Liverpool to Manchester Airport service (Newton-le-Willows, Oxford Road, Piccadilly and East Didsbury/Heald Green only)
Arriva Trains Wales:
Llandudno to Liverpool (via the Halton Curve)
Swansea to Manchester is much faster
Chiltern:
London to Birmingham Express (90 minutes): Bicester North, Banbury, Leamington Spa, Birmingham Moor Street
ScotRail:
Aberdeen express from Edinburgh, calling only at Haymarket and Dundee.
2tph Edinburgh to Perth (Haymarket, Stirling, Dunblane, Gleneagles (1tph), Perth). This would extend up the Highland MainLine every 2 hours.
1tph Inverness to Dingwall extending to Tain, Kyle of Lochalsh or Wick (each route every 3 hours)
CrossCountry:
Newcastle to Plymouth (1tph), with extensions either end every 2 hours to either Aberdeen or Penzance:
Stonehaven, Montrose, Arbroath, Dundee, Leuchars, Kirkcaldy, Inverkeithing, Haymarket, Edinburgh Waverley, (Berwick-upon-Tweed,) Newcastle Central, Durham, York, Leeds, Sheffield, Derby, Birmingham New Street, Bristol Temple Meads, Taunton, Exeter St Davids, Plymouth, Liskeard, Bodmin Parkway, Par, St Austell, Truro, Redruth, Cambourne, St Erth, Penzance
Manchester or Leicester to Bath Spa or Plymouth/Paington (the way the paths have worked out, they can't work Manchester-Plymouth/Paignton or Leicester to Bath Spa, so there has to be some asymmetry)
Nottingham to Glasgow Central (via Leeds, Newcastle and Edinburgh)
Virgin Trains:
Glasgow Express (calling only at Preston and Carlisle)
TransPennine Express:
Nottingham to Liverpool: Derby, Chesterfield, Sheffield, Hazel Grove, Stockport, Manchester Piccadilly, Manchester Oxford Road, Warrington Central, Liverpool South Parkway, Liverpool Lime Street.
Manchester to Edinburgh: Huddersfield, Leeds, York, Darlington, Durham, Newcastle Central, any 3 of Morpeth, Alnmouth, Berwick and Dunbar, Edinburgh Waverley.
Liverpool to Edinburgh: Wigan North Western, Preston, Lancaster, Oxenholme, Penrith, Carlisle, Lockerbie, Haymarket, Edinburgh Waverley.
Manchester to Glasgow: Pretty much as is, but with an additional stop at Carstairs
Greater Anglia:
2tph Norwich to Great Yarmouth (1 all stations, 1 non-stop)
2tph Norwich to Cambridge (1 with a varying stopping pattern, 1 express, which continues to Stansted Airport)
1tph Peterborough to Harwich International
4tph London to Cambridge (1 semi-fast, 1 stopping)