The railway does seem to go in cycles.
For a while, the plan was rationalisation, one TOC per London terminus, splitting long established services to make supposedly "neater" franchises (e.g. Wales & Borders) - keep it simple, stupid.
But now, things are going the other way. e.g. whilst it makes sense to have a second Scarborough - York service per hour, I can't see the point in giving it to Northern (creating a second TOC on that line).
So we have a situation where TPE are being stretched into new markets (ECML north of Newcastle, Liverpool to Wigan) but then being backfilled by Northern taking a presence on TPE routes.
It'll go back in five/ten years time, and someone will decide that it'd be simpler to have just one TOC running north of Newcastle, and we go round and round...
Well even the LNER services North of York suffer from overcrowding at times so there's definitely demand there, in terms of XC the two services serve different markets anyway - that via Doncaster is more for Newcastle/York to Birmingham being about 20 mins faster than the service via Leeds, and the service via Leeds primarily serves the Leeds - Newcastle/Edinburgh and Leeds - Midlands and South West markets, and has quite high passenger turnover at Leeds itself.
In your ideal world no two places more than about 50 miles apart would get direct trains anyway so it's a good job you're not involved in service development/timetable strategy isn't it
As you've said yourself, the majority of passengers on the "via Leeds" service seem to get off/on at Leeds, so chopping the service there wouldn't inconvenience most passengers (and the passengers travelling from stations other than Wakefield would still have the faster "via Doncaster" journey) - there's two TPE services per hour from Leeds to Newcastle (hourly to Edinburgh), so removing the XC service north of Leeds would only be going back to the situation passengers were in before TPE doubled their Newcastle services.
Leeds would retain its hourly service to the Midlands, so really the only inconvenience would be Wakefield passengers heading to York/ Newcastle/ Edinburgh (who I'm sure exist but I'd put the needs of people crammed into Voyagers south of Wakefield above the need for ten Voyagers at a time being north of Leeds).
Those 4-5 car trains are a waste, I think we'd be better off with less but longer trains north of York
Agreed
Doubling up TPE services formed of the Nova fleet isn't going to work because of platform lengths (and of course the fleet isn't large enough)
There's a production line at Newton Aycliffe that'll be looking for work fairly shortly...