Put it this way, if every train had 8x23m coaches, it wouldn't matter if the Scotland trains stopped at Bolton or not. There is plenty of capacity between Manchester and Stockport.
However what you will get on these services will be 4x20m coaches a lot of the time. This is not at all sufficent to carry anything more than a small flow of Bolton passengers in addition to the very large flows between Manchester and Cumbria + Scotland that have been developing of late. It is not a nice experience starting your 3-hour journey stood up crushed against the wall with all of your luggage etc because there are a large number of people using the train because it is the fastest way between Manchester and Bolton.
Of course, it mightn't be such a problem if sufficient capacity were available on other services, but isn't Manchester - Bolton still running at slightly less capacity than it was before the change? I'm very surprised at the assertion that 'few' people were unhappy with the previous setup as the Bolton Commuters vs Socts argument got going on here more than a few times!
As for stopping anywhere between Bolton and Preston you can forget it. Is this an inter-city service or not!?
