The "forced overnight" in the middle of the route probably hurts the Skeena. The other thing that jams it is the fact that there isn't exactly a good way to get away from Prince Rupert except to take the train back to Jasper, not to mention that the train connections in Jasper aren't great (though admittedly they could be worse, IIRC the Skeena doesn't connect with the Canadian either way, so you've got either one or two nights in Jasper if you're trying to do your trip entirely by train).
Honestly, if you wanted to improve the performance of the Skeena you'd either [A] restore the link with the Canadian in some form, tweak the ferry system to allow some effective way out of Prince Rupert, or [C] extend the train to Edmonton (which at least has a decent airport to speak of). Doing that should pick up some decent Edmonton-Jasper traffic as well as making the tourist trip on the train a bit more workable insofar as it wouldn't require extremely wacky transfer games to get to a decent airport.
Edit: Well, I checked the schedules, and none of the Canadian-Skeena connections work and you have a bunch of two-day connections. The Skeena arrives after both have departed and departs before either arrive. If there's anything that could kill the Skeena's performance I'm going to suggest that this is a big one. So...
Skeena arr. Jasper 1830 (Thurs, Sat, Mon)
EB Canadian dep. Jasper 1730 (Sat, Mon*, Wed)(no connection)
WB Canadian dep. Jasper 1430 (Fri, Sun*, Tues)(no connection)
Skeena dep. Jasper 1245 (Wed, Fri, Sun)
EB Canadian arr. Jasper 1600 (Mon*, Wed, Sat)(no connection)
WB Canadian arr. Jasper 1430 (Tues, Fri, Sun*)(no connection)
If I arrive on Tuesday's Canadian from Toronto, I can take the Skeena on Wednesday. If I arrive on Friday's, I have to wait until Sunday; if I arrive on Sunday I have to wait until Wednesday. If I arrive from Vancouver on Monday, I have to wait until Wednesday; a Wednesday arrival dictates a wait until Friday and a Saturday arrival at least allows a next-day departure on Sunday.
Arriving on the Skeena, to board the EB Canadian I have to wait two days, full stop. The only set of the four connections that is really at least passably sensible is boarding the WB Canadian: In all three cases, I can board the next day's Canadian bound for Vancouver.
FWIW, Charlie Hamilton and I have wanted to do the Skeena for a few years. This discussion should give y'all a hint as to why it has not happened, and I highly doubt that we're the only ones in our boat.