Manchester - Scotland services have used the Bolton and Chorley lines for many years, long before TPE was thought of. I blame the diversion towards Wigan primarily on incorporating the Scotland service with the Barrow and Windermere service which meant Scotland trains became much busier with local passengers. This was in 2007 when Virgin ran a 2-hourly service (though in essence it was still a 2-hourly service albeit with extras in the peak hours up until May). Ideally, upon electrification and higher line speeds, Bolton should go back to having two inter-urban semi-express trains per hour as it did in 2007, re-route the Scottish services via Bolton but running every hour and non-stop from Manchester to Bolton then non-stop to Preston. Wigan retains two Scotland trains per hour plus a third if Liverpool goes on the map, more than enough.
The two semi-fast inter-urban services should be the electric Blackpool which could also work as a portion train, the other half going to Windermere (if this branch is electrified) and a faster diesel service to Barrow using 185s.
All this talk of the Mid-Cheshire line and the Sheffield and North TPE lines needing more trains, well so do Bolton and Chorley and I think these two have a bigger case than some seeing as they have had a service taken away in the last year.