I think you are mistaken. Terminations short at Stalybridge are still happening daily, often several times a day.
Missing stops in order to make up time is not new. That, too, has been happening regularly since the timetable change.
The specific example you give, of the stopping train between Leeds and Piccadilly calling only at the principal stations which are also served by the expresses, shows the mind-numbing stupidity of it all. The main purpose of this particular service is to get commuters from Marsden, Greenfield and Mossley into Manchester, so skipping those stations makes it close to useless.
Today has been the worst day yet since the timetable change, with 11 out of 42 trains at Slaithwaite being cancelled (have included part-cancellations in this).
TPE have had eight weeks to show that the new timetable can be workable, and it's just as bad as on day one. From a passenger point of view (and it's clear that there are some in the railway industry who see passengers as at best an irrelevance, at worst a pest), it can't go on like this and needs to be changed long before the May 2019 timetable change.