Bradford to Skipton was simply split in two (and the Skipton services then split up into the 66 and 78A, the 66 being fast and the 78A going all round the houses).
Bradford to Ilkley is a bugger to do (especially with the 653 being withdrawn).
There's still one a day from Bradford to Worth Valley villages on the 698, but there did used to be 4 an hour (3 via Keighley).
However the Bradford to Skipton and Worth Valley buses used to wait 10 minutes or more in Keighley bus station - I remember missing a bus, getting the next one to Keighley and running to the next stop to catch the one I'd missed a few times.
A tendered Halifax to Keighley bus is currently being considered (with operators having submitted tenders).
I suspect most of the express passengers from Leeds to Sheffield moved onto National Express - at one point they upped their frequency to every 30 minutes on that section of route.
I'm not sure a Leeds - Bradford via Yeadon is the most obvious missing link - though there's a distinct lack of buses between Bradford and Guiseley.
Skipton to Harrogate would be a very useful link.
There are buses between Harrogate and York - with a choice of routes. No quick ones, though.
http://www.yorkbus.co.uk/cmsUploads/route/files/littleexplorerAug16web.pdf
http://www.connexionsbuses.com/content/uploads/2017/02/412-X70-York-only-07-11-16.pdf
There's also been a massive loss of express services - the X36/37 were well used by me between Halifax and Huddersfield, as was the M62 between Halifax and Leeds. I do remember
Of course many of the routes you list saw massive improvements in the parallel rail routes. Of course some people, living some distance from a station, would prefer the bus, but many passengers simply transferred.