You mentioned staged trains for a heavy mainline, so that might be somewhat different from what is in-view on the layout.
In my own case, I want to model a small (fantasy) shortline that interchanges with the B&O mainline somewhere between Cumberland and Connellsville. Many of the B&O trains, both freight and passenger, do not interact with the shoreline, but they visibly go by. A few other B&O trains stop at the station at the interchange for passengers, express, or freight car interchange. The trains that just "go by" are still visible on the layout for nearly 2 scale miles.
The way I approach designing my inventory is to first figure out how many cars I want to move around each session on the shortline. Figures like 1/2 or 1/3 of the available car spots are typical for supporting that part of the calculation. Of course, I need enough shortline yard space and interchange track length to handle those cars actually being moved, so if the yard would get too full to move cars around comfortably, then that might become your limit for how many industries you can service per session.
Then, for the B&O trains that interchange cars, I have to decide how many trains will be doing that. Typically, there is a local freight going by each direction each day, plus a coal shifter or two, and maybe a "turn" train that comes to pick-up special cargo (in my case, reefers full of beer), and maybe some express car setout and pickup. I need to decide if I have enough staging track length and locomotive tonnage rating to have other cars "for show" in each of those trains besides those actually interchanged.
Finally, I need to decide how much to have in staging to simply "run through" to simulate other mainline traffic. That is really a function of remaining staging space. In my case, I just must have an EM-1 pull 50 hopper cars through the scene every so often, or it would not seem like the B&O mainline. And, then there are scheduled merchandise trains, extras with perishables, ore trains, "stone" trains, and the scheduled passenger and mail/express trains. As you already stated, some trains in staging have to do "double duty" or more to make a reasonable level of Class 1 mainline traffic with the amount of staging we can actually have. But, whatever staging you have will probably be close to 100% full, with maybe one extra track left open.
In my case, I am currently not able to finish the area where I intend to build my layout, so I have a lot of time to plan (and fanticize). I am doing that with a pair of computer programs that (1) allow me to design track plans and export them to (2) a program that lets me populate the plan with cars and simulate running the trains. (I use AnyRail and TrainPlayer.) This has allowed me to iterate my thinking on design, operation and inventory so that I can refine it to suit my space, tastes and budget.
But, yes, I have already acquired some things that I already know don't fit my evolving plans. It happens to everybody, I am sure. Sometimes, just the availability of a new and attactive model changes my plans (e.g., that EM-1).
