1. Stepping up to an hourly Crewe-Salop would be expensive, but might allow the Manchester-South Wales trains to be speeded up (but at the expense of longer distance passengers at Nantwich/ Whitchurch).
2. Linking the shuttle to other services introduces significant performance risks.
3. Platforms on the Independent Lines would be awkward to build and some distance (laterally and vertically) from the rest of the station at Crewe. Currently if you're travelling to London/ Birmingham/ Scotland it's often cross-platform or a bridge to a platform in your sightline. Go to the Independents and it's a trek.