I'd say that one of the best schemes I can think of would be:
Wigan Wallgate - Wigan South Junctions
Wigan South Junctions - Ince - Hindley - Westhaughton - Lostock Junction (With new platforms at Lostock Junction for the Wigan Line, and extention of all platforms on the Manchester NW elecrified routes to at least 184m (8 x 23m) toward preston ready for doubled up 319s and 92m towards Wigan for single 319s.
Salford Crescent would also need some looking at, since service levels could soon be 14tph in each direction through Windsor Bridge Jcns
While we're on the subject of Greater Manchester, some more wiring that might sound silly on it's own but is quite sensible when you think about it, and add some more platforms at a couple of stations.
Victoria - Stalybridge (Increase the number of platforms at Stalybridge to 4)
Victoria - Ashburys (Two bay platforms to be added at Ashburys, or Four Track to Guide Bridge)
Victoria - Rochdale (With more bay platforms at Rochdale)
This would allow a great amount more capacity in Victoria, one of these may not be needed for the services still Diesel from the West.
Electric from west:
Wigan Wallgate via Bolton 3tph
Preston / Blackpool North via Bolton 1tph
Liverpool Lime Street via Earlstown 2tph
Possible additions:
Horwich Parkway via Bolton 2tph (Peak)
Diesel from the west:
Southport & Kirby via Wigan Wallgate and Walkden 2tph
Clitheroe via Blackburn and Bolton 1tph
You can proberbly guess where this is going to create a timetable where no services terminate from the West at Manchester Victoria, with only longer distance services from the East terminating, such as Manchester Victoria - Huddersfeld 1tph and Manchester Victoria - Leeds via Todmorden and/or Brighouse 3tph making use of platforms 1 and 2 in Victoria.
With wires from Ashburys to Victoria some of the Hadfeild / Glossop or Sheffeild services can run to or through victoria to have better cross manchester connections without having to change trains. For example, Glossop - Blackpool North.
I've ranted too much now, but some short extentions to Rochdale and Stalybridge can free up capacity in Victoria, and if Lostock - Wigan where electrified, only 3tph would be left as diesel through Bolton. (Manchester Airport - Barrow / Windermere and Manchester Victoria - Clitheroe and Manchester Airport - Southport), that would be increasing capacity as electric stock tends to have more similar charicteristics, and the diesels travel Crescent - Bolton non-stop.
Still, this idiot wants to see the Leigh - Tyldsley - Walkden route re-opened with 2tph Victoria - Leigh giving Walkden 4tph into Manchester...
Some other sensible areas would be extending the 3rd Rail from Kirby to Wigan Wallgate, and Southport - Wigan Wallgate. Make better use of dual voltage 319s anyone?