I think these through services have been running about three years. I suspect they would do more, but on weekdays they would entail blocking all lines at Leeds (please correct if I'm wrong) - so there isn't the capacity to do so. On Sundays, they can get away with it, so why not run a through train if the diagrams allow it? It might attract a few extra punters, after all?
You are right the trains - from Sheffield and Preston, returning to Nottingham and Blackpool respectively - are popular and attract extra passengers.
Its often forgotten when people discuss the line that people live here and some of us use it regularly / daily. We have to be the core group Northern must facilitate all year, along with seasonal / weekend walkers and the silvers - maturer people, usually couples - without whom daylight hour trains would be pretty empty during the Autumn and Winter months.
As presented the 09:17 would certainly need to be a four car in the Spring / Summer as the 08:47 is a very busy train. Its usually a crowded 158+153, and when theres no 153 it can be standing from Settle. Three morning trains from Leeds reduced to two is a clear worsening of service.
There remains considerable commuting through the Eden Vally between Appleby and Carlisle, using the 05:19 from Leeds, which survived the Eden Brows closure as Northern laid on truly good quality and well-timed coaches.
Condor7 is right that its very useful to actually have a slightly faster train to get to Leeds or Carlisle. Summer visitors forget how short our daylight hours are out of season; it seems an ever longer journey when the landscape is in darkness. A case can always be made to make 1M53 / 1E23 a stopper, but that ignores their use by locals, day-trippers and through-travellers.
A standard single from Leeds to Carlisle (and vice versa) is usually available for around £15 and is both quicker and cheaper than via Lancaster (£48) or Manchester (£32), and doesnt require a change. Its certainly a viable passenger through route between Carlisle and West Yorkshire, and vice versa, which wed all like to see extended to Glasgow. The first time I ever travelled over the line was on the 23:59 from Nottingham to Glasgow in the summer of 1974 - I wonder how many times I have glimpsed the Ais Gill Summit sign since then.
The 60mph speed limit is perceived as hindering the S&C, of course. The current gaps in service are also considerable and can, therefore, be a deterrent too. FoSCL have worked really hard to see something from Leeds fill the weekday gap between the 14:49 and 18:06 departures, which the latest proposal does address; and one from Carlisle between those leaving at 05:50 and 08:53, which is ignored - but is particularly relevant to those of us who live here.