Many early railways were built for freight, rather than passengers. So, there would be lines built to serve coal, iron ore, stone & other mineral production areas, linking them to towns & cities, and also to manufacturing centres (existing or new) outside major towns. Passenger traffic was almost an afterthought with these early railways. Many of these would have closed as mineral sources became exhausted and manufacturing centres declined.
Passenger services developed initially to link the larger towns & cities. Smaller towns & largish villages may have received railways gradually , but there would have been no competing lines providing two or more railways to many of the smaller towns - no cases of 2 or more railways running in parallel along some of the Cardiff /South Wales Valleys, for example. Some routes might not be the most direct, being designed to serve the greatest populations, rather than to provide the fastest journeys.
So, as just one of many possibilities, there might have been a West Coast line from London (North Central) - Northampton - Birmingham - Stoke - Manchester - Preston, etc., with a Stoke - Liverpool branch. Towns like Nuneaton, Tamworth, Lichfield would be served by east/west lines starting in Birmingham. London - Leicester would be served mainly via Northampton or Rugby, but a secondary route (like a MML) might have been created from London to serve growing towns like Luton, Bedford & Kettering.
Towns like Warrington, Wigan would probably be served by branches from Manchester or Liverpool - only one of which would be a Liverpool - Manchester route.
Blackpool may have remained a tiny seaside village without a railway, a few miles from a line from Preston to the once important port of Fleetwood.
An East Coast route might have started from the same London (North Central) terminal and run via Cambridge, Peterborough, Lincoln, (then Doncaster or Sheffield) to Leeds, then York, Darlington, Newcastle, Berwick & Edinburgh. Branches would serve the ports of Grimsby & Hull (Immingham would probably never have been built.). There would be at most 2 cross-Pennine routes - possibly Sheffield - Barnsley - Huddersfield - Manchester & Leeds - Bradford - Rochdale - Manchester (a bit like the Calder Valley, but Bradford being on a direct line with no need for reversals) etc., etc., etc.....