If the core decisions about NPR are political and essentially arbitrary, then it'll give the scheme a torrid time getting through all the stages to delivery. HS2 was an interesting scheme in that no one was ever really able to articulate a different coherent vision. As soon as you accept that you can't just upgrade the existing WCML, MML and ECML it's pretty much inevitable that you'll end up with a Phase 1-style line linking Euston, the Elizabeth line/Heathrow to the West Midlands and the WCML. A decision like going via Huddersfield or Bradford seems much more controversial, especially when local politics make it difficult to prioritise one centre over another.
Like I've been saying in the Phase 2b East thread I think it's better to think about NPR as a massive scheme to use new lines and other major interventions to make the current rail network work much better. It seems entirely sensible and achievable to build a network designed around 200m long classic-compatible trains capable of running at 230km/h (maybe up to 249km/h if there will be long stretches of shared HS2 mainline running). With that, you have the flexibility to use existing stations and lines in areas where that's achievable and worthwhile. It'd be just fine to have a fast tunnel under the Pennines and then send some trains onto a loop into the existing Huddersfield station.
The problem of the four competing (with Leeds obviously in front, but not being dominant enough to make the others irrelevant) urban areas of West Yorkshire can be better dealt with this way. Provide some sort of express route connecting each of them together, even if that means four-tracking some bits of classic line used today. Then link your fast TransPennine line into this web of upgraded tracks. You can then run whatever sorts of services you want. Manchester to Leeds via both Huddersfield and Bradford depending on what service you get, and so on. If it's going to be too expensive to four track or add new fast alignments, but it would be possible to use the current line for faster trains, then build a cheaper metro network in parallel and close the existing local stations.