I priced an USA transcon as follows:
Y: $150
C: $520
F: $500
My LF for Y is typically around 85%; C is 40% and F: 10%. There isn't really demand for F on the route, but the fact that F is cheaper than C, one would assume that passengers booking C would instead take F because it is cheaper.
Is there anything that can be provided to help justify the behavior of passengers better when purchasing tickets?
The passengers in the simulation simply are not as smart as you would think. They do not consider the possibility that F might be cheaper than C.
how much of an impact does time of day and length of flight have on a schedule? Additionally does a pax weight one airline higher based on frequency of flights? (ie if airline a flies a route 10 times vs airline b one time - does it make a difference to pax?)
There are ~10-15 different variables that affect how they choose the flight, and all those you mentioned are modeled. But 'how much' each thing affects, is not fixed, or can't be just told directly as it's quite scalable.