Much of the Great Western operation seems to be designed to serve the needs of those Thames Valley commuters rather than anyone else. The high-density HSTs now seem to be used interchangeably with the low-density ones on the real long-distance routes, there are Penzance trains with only a single first-class vehicle -- all apparently so that the government can deliver its "seats for commuters" promise. I think you're so right that the answer on the GW is that separate fast Reading service (though there might be a case to run it out to Swindon).
The German system works very well, passengers understand it, and you rarely see a need for anyone to be excessed during the regular on-board ticket-checks.
But even if we decided to go that way in this country, do we have the track and platform capacity to do it? Could the approaches to Paddington handle two extra fast trains per hour each way (particularly east of Airport Jn) and are there enough platforms? And we're all well aware of the capacity problems in the Birmingham, Leeds, and Manchester areas. And we've discussed Trans-Pennine's frequency here often enough. Do we really need 6 trains an hour, or would, say, four fast trains an hour and a proper local service (which might well need infrastructure investment) be a solution that might actually serve all passengers better? How do such questions get discussed, let alone answered, within the structure of today's railway industry?
It's a bit to do with lack of infrastructure, but also to do with lack of political will. As the ludicrousness of Thameslink Wimbledon Loop services shows, people value direct services above better services. If we look at the North TP Mainline, the German system would likely see
2 IC trains per hour, Newcastle, (Durham, Darlington)*, York, Leeds, Manchester Vic, Liverpool.
2 RE trains per hour, York, Leeds, Dewsbury, Huddersfield, Stalybridge, Manchester (Ordsall Chord Stations), Manchester Airport
2 RB trains per hour, All Stations Huddersfield - Leeds
2 RB trains per hour, All Stations Manchester Vic - Huddersfield.
2 RB trains per hour, All Stations York - Leeds
Hull, Scarborough, Middlesbrough would all be operated as branches of the ECML, with connections at York/Leeds (probably at 2 tph RB each).
That's still 6tph along the main "core" route and could (probably) be flighted as IC - RE - RB each half hour (not that I've made a timetable here or anything, it's largely guesswork).
But, your Hull, Scarborough and Middlesbrough passengers would complain they'd lost their direct service to Manchester and people from Church Fenton would probably complain about their lack of Blackpool trains. The nature of understanding of the railways means that people will value 1tph direct over 2tph with a good connection, regardless of the fact that it's a much worse service.
*I've included Durham and Darlington here, because they generate similar passenger numbers on the ECML and we're talking about not changing infrastructure. I think in a German system, there'd be 4 tracks Northallerton - Newcastle, which would allow for a more frequent RE service from York - Newcastle all stops (Chester-Le-Street, Durham, Darlington, Northallerton, Thirsk), probably with Durham and Darlington getting an IC service as well, but not the full thing.
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