Of course having through cars is better than not having through cars and having sleepers is better than not having sleepers etc. That is not the point. I think we spend to much time and effort trying to gold plate everything to the point that it all becomes cost prohibitive and is dropped. We should be able to be more agile in grabbing opportunities to start a service rather than wait for perfection. Irrespective of whether lack of through cars hurt ridership on the Pioneer and Desert Wind or not, people had service in those routes for several years which they would not have had if everyone waited for perfection back then.
My concern isn't getting a "perfect" situation, it's avoiding a major bust. I'd hold up the Spirit of California as a great example of lousy equipment allocations ultimately killing a train: I've been told that the train regularly ran with two sleepers (usually sold out or pretty well-sold) and several coaches (mostly empty for the overnight chunk of the trip), contributing to the train only hitting about 50% of its ridership target and falling short on revenue. The result was that the train was unable to survive when a round of cuts came (albeit from the state, not the feds).
In this case what I'm worried happens is the Flyer gets extended as far as Newton and you get a
lot of passengers who wonder "Why in the [bleep] would I want to go to Newton?" To their credit, yes, Wichita would get service; what I
really want to avoid is getting a lousy service that lasts a year or two before someone decides that it's cheaper to refund the Feds than it is to keep running an empty train. Don't forget that the Desert Wind and Pioneer weren't subject to line-item funding.
Also, I'm looking over the timetables for them and it looks like there were through cars by 1982 (I see explicit mention of a through coach for both trains and the timetable
seems to say that the sleepers are Chicago-Los Angeles/Chicago-Seattle by then (the coaches are listed as originating in SLC/Ogden except for a thru coach on each train); in the 1981 timetable it indicates the thru coach but the sleeper is explicitly "Salt Lake City-Seattle/Ogden-Los Angeles". Basically it proceeds from being "connecting trains" with decent hours in 1980 [1] to through coaches in 1981 to sending a lot of stuff through in 1982 (coincidentally or not, when Claytor took over).
What this tells me is that making a bunch of sleeper passengers change trains was
not a winning move, even during the day. I can't speak to the ridership numbers in 1980, but somehow I do not think through traffic was blowing the doors off at that point and there's a good chance that Amtrak was more "not in a position to axe the trains" (the Desert Wind was the result of a lot of pressure from Howard Cannon and brought to you by the number 51) than keeping them for their stellar ridership stats. As to running an overnight-ish train without a sleeper, the only other real example of that I can think of is 66/67.
As an aside, a picture of some Desert Wind consists from the early years shows the most motley mix of equipment...I see a Heritage baggage car, Heritage sleeper, Amfleet cafe, Hi-Level coach (I strongly suspect it was a step-up coach), and two Superliner coaches. Wow.
Back on topic, my feeling is that though it would be lousy practice from a connectivity standpoint, the FTW-KCY day train is probably the more feasible of the two. Realistically it would probably be better to run both trains to KCY (where the overnight train would allow a through connection to the SWC/River Runner) but everything I have seen says that the extended Flyer would perform poorly next to the daylight through service if I have to pick one.
[1] 2300 WB and 0700 EB are roughly what you're looking at in this era. 2300 isn't
great (it's what we have now) but 0700 is a heck of a lot better than the 0300 we have today. Compare that to 0150/0420 in the timetable for this train...