That only applies if they are actually going to Leeds/Manchester and not changing to another train at Leeds/Manchester. If they are connecting to another train they'll probably use which one a journey planner tells them to - or the one before if they want to be on the safe side.
When it goes to 6tph passengers will probably care more about which train they catch. It's possible some of the semi-fasts will get overtaken, while if they need a connecting train it will depend which station it departs from.
I'd hazard a guess that the majority of passengers getting on Eastbound TPE services at Huddersfield will be getting off in Leeds, whether that be their destination or if they're catching a connecting service. If they are travelling further and booked online, they most likely won't have considered what type of train it will be, as much as that seems strange to members of these forums!
A significant number though, will be heading to the shops in Leeds with a DayRover or an ordinary walk-up ticket. It seems to be this group that might reduce the strain on the TPE services if they could be persuaded to take the stoppers. If Northern ends up with a few EMUs to the standard of say the 318s, the Leeds-Huddersfield stoppers might see a fair few more end-to-end passengers- Unlike the HUD-MCV stopper, they will most likely stay.
As I understand it, the 'semi-fasts' East of Huddersfield will most likely only serve Dewsbury (at 2tph, the same as today). It's to the West of HUD that there's more capacity issues which lead to the all-shacks stopper being withdrawn. I do think that a fair few passengers will avoid the semi-fasts heading West, though that could well be balanced by a fair few that currently baulk at getting a Merseytravel 142 but will go for a slightly faster 185/170.
There may be no option but a mixed fleet for North TPE if Hull doesn't get electrified by December 18 or if the next franchise operator wishes to retain some through services to Middlesbrough and/or Scarborough, the consultation asks whether any through services such be retained and if applicable how many should be retained.
A mixed fleet during the transition from diesel to electric is unavoidable (it may be slightly less mixed if the 170s do go South!), but in the long(er) term electrification to Hull is very likely.
Scarborough was originally planned to transfer to Northern as an extension of the Copy Pit service, though as I understand it the ITT for both new franchises leaves this to be decided. I'd argue that the Copy Pit extension is the 'least-worst' option- and would see mainly 158s or possibly even cascaded Turbostars in the longer term, which many passengers would probably see as an improvement!
Middlesbrough is a bit more tricky, but with bi-mode IEP coming, trading 1tph to Leeds & Manchester for 1tp2h to London (perhaps an extension of the current York terminators- though the timetable is likely to be quite altered once the 800/801s are in squadron service) doesn't sound too bad- particularly if a semi-fast (current TPE stops) DMU shuttle to York could run in the other hours. There's also the possibility of diverting CrossCountry's Newcastle services.
Well that's because passengers are effectively told not to use them. The services are advertised as Bramley/Bradford Interchange at Huddersfield and as Deighton/Brighouse at Leeds. Journey Planners don't show them as they are overtaken (unless you specifically ask for overtaken services to be displayed.) Posters at Huddersfield station say something like "Travelling to Leeds? Then catch the trains bound for Newcastle, Middlesbrough, Scarborough, Hull and York."
That must be a new feature (perhaps since the recent timetable change?) for the services via Dewsbury, as I've not noticed it. The via Bradfords have always been advertised at both ends as serving the penultimate stop- though in the last 18months or so they've been advertised at HUD as Bradford rather than Bramley.