Many of the problems are due to too much “gamification” or lack of realism. Running costs are a typical example: in real life there is no single “running cost”, there are separate fuel, crew, periodic maintenance and load-dependent wear and tear. There is also a choice between replacing and refurbishing aging equipment.
RL equipment does not run non-stop, it has at least a daily turnaround pause to get cleaned, refuelled and inspected. Horses need frequent rests and fodder. Steam locomotives need frequent watering and a load of coal at the end station. The amount depends not just on distance, but very much on the load. A heavy freight train running uphill will need a lot more fuel than a light train on level track.
If all that, as well as replacements or upgrades, could be automatically handled with upgrades based on per line, per type or whatever user settings, everything would be both more realistic and more enjoyable. It would need a more sensible (much slower) timescale, though.