Shameless plug:
I've written a 2 part article about HS2 on my blog.
Part 1 - Why HS2 is Required
Part 2 - The PR Failure, and the Damage of Deception
Feedback etc. appreciated, especially from railway insiders who can spot the errors I have most likely made.
I like the way you have presented your reasoned and measured assessment of the case, but I'm not convinced!
If its about capacity and not speed, then it would surely have been more sensible to use the proposed freight only route to remove much of the freight from WCML. Think it went along part of GC, Woodhead and across to Manchester and Liverpool. This would have been cheaper, would have been less disruptive as the line would only have needed to be 100mph and could therefore be more twisty.
The WCML is at or near capacity for only a very short period each day - morning into London and evening peak out. Much of the rest of the day its got considerable capacity, with long commuter trains carrying fresh air. The answer here is not to build a new railway, but to change work patterns, where offices are situated in the country and stop the London focus. This is a political imperative.
HS2-Phase 1 is really an extended commuter route for business people in Birmingham - the flows will be markedly towards London in morning and back in the evening. Its London businesses wanting to offer people cheaper housing by living in Birmingham and not having to set up offices in Birmingham. Londoners won't be seen dead in Birmingham unless forced. It clearly is nor was ever about speed to Birmingham.
HS2-phase 2a & 2b were a sop to the north to get Parliamentary and business approval for the vast expenditure on the Phase 1 commuter route. Slowing down the trains maximum speeds to save money means that Phase2a & 2b + any extension to Scotland will take longer (but happily that doesn't really affect Phase 1 significantly). Once north of Birmingham, because of the greater speed than at present, there will be few stops and the benefit will really be for business people. The general public has a lot more flexibility at what time they travel, but having a branch line to get to Sheffield (when it should be a through service), seems a dead end proposal.
As Phase 1 is almost certain to be way over budget(if not cancelled very soon), the likely result is that one or both of Phase 2 a or 2b will get cancelled (probably both) as "clearly we have to finish Phase 1 as its already being built". The rest of the country suffers from not having a single massive destination like London. Instead it has Birmingham, Liverpool, Leeds, Manchester, Newcastle etc most of which cannot be connected on a fast straight line from north to south or indeed east to west. NPR then tries to fix this, but how could connecting them only seem to spring up now? Transport planning in north is a victim of geography, topography and political issues. The political comes as in Bradford being on NPR route. Sure, its a big city and its poorly rail connected with most services going via or to Leeds and two separate stations. But, its a very challenging route, extortionately expensive and in railway terms you would want to avoid it. The local population is unlikely to generate vast numbers of trips, particularly as most trips are relatively local at present. Deprived people in Bradford are unlikely to want to travel to deprived Liverpool for jobs. HS2 only going from Leeds or Manchester means that Bradford people would have to change trains anyway to get to London, hardly a time saver. The impact of HS2 on Bradford is that businesses will move to Leeds (indeed HMRC is already doing so (from Bradford and Shipley) as is Royal Mail (Bradford). Faster rail journeys tend to benefit a dominant place with higher land costs and create a suburban commuter belt form lower cost areas. Lack of suitably qualified staff, lack of entertainment, high crime mean that Bradford will only likely be an origin of choice, rather than a destination.
The slowest part of the journey south from Leeds on existing tracks is from Leeds to Doncaster and worse, Leeds to Sheffield. The dead end at Sheffield on Phase2b doesn't seem to help with this at all. The existing lines could be beefed up some 4-tracking and much straightening and underpinning in mining areas to significantly improve many journey times, not just those to London. It is ridiculous that local trains take so long to get from Leeds to Sheffield. Leeds to Birmingham is also currently very poor, but Birmingham is a Dead end again - if it were for the north as well as London, they would have made Birmingham Curzon street a through station. By the way its being done, as I understand it, a passenger from Leeds to Birmingham is going to have to go to the International station and the connecting service to get to Birmingham itself. One from Bradford to Birmingham will have two changes if I've understood it correctly.
Manchester is more interesting, but if it avoids the airport (can't remember) phase2a will miss out on the clear opportunity for rail transfer from London to Manchester airport if Heathrow 3rd runway is scrapped.
There is a political maxim. "The farther away from London, the less concern we have"