Regarding some of the elaboration here:

Put back the combat penalty when units overlap
- I'm not sure this applied with RTW and the historical style of battle during that period.
This is one of the most important things that need to be fixed. This means you can lump all your cav units together in one mass and win vs an opponent that will try to pin and flank you. The importance of this can't be understated.

Aren't these already the case:
Provide more settings on fatigue rate, morale level, and ammo
Separate the fatigue, morale and ammo settings
No, you don't have multiple selection regarding these, it's a "use it or leave it" approach. If one wants to play with fatigue, but not with the standard fatigue system that doesn't penalize enough (as in MTW/VI for example) running around, then no other option exists. Same thing with the other settings, some people don't want to use upgrades to most units in order to bring them to a desired general morale level, and sometimes the upgrade system works contrary to intuition and number-crunching methods ("army selection skills") become more important than the actual use of your units.
With ammo it's maybe harder more settings (like 1/2, 1/4, x2 ammo?), but we 're not talking mainly about an arrow exchange with the AI, but rather vs intelligent players, where you might be relunctant to move unless the opponent has used a good portion of his ammo/ tired his shooting units. Now, if this means 15 minutes of non-stopping, pure shooting, then it's something that can alienate a portion of the players (I can speak of VI here), that consider it an extremely long time, given that over time units start becoming less effective, slowing further the combat resolution phase. Just to be able to cater to different tastes without small modding that makes games incompatible.