If NPR does go via Huddersfield, then the existing Leeds - Bradford - Halifax - Huddersfield services becomes to a degree redundant. If this does indeed happen I think it might be an idea to put the bay back in at Sowerby Bridge and run direct trains to Huddersfield.
If platform capacity becomes an issue at Huddersfield, then I would look at the feasibility of re-instating at least part of the Clayton West branch to Skelmanthorpe. Since its single line I don't think sharing the old trackbed with the 15inch Kirklees Light Railway is going to be much of a problem.
Then at least stations at Berry Brow, Honley, Brockholes, Shepley could also benefit from an improved train service.