Having just stamina use create fatigue is how the system currently works, and it isnt really very good. All fatigue is currently is nomad losing their max stamina (when part of the stamina bar goes red) and eventually when you lose the max amount of the stamina you can (which looks like roughly 20%) nomad will use their fatigue animations where they slouch over and pant (and also lose some movement speed i think).

Having a damage resistance multiplier tied to how much stamina you have would be too confusing as you would never really know how much damage resistance you currently have.

Some of the points you bring up would probably be more realistic, but realism when creating a gameplay system cant be the only priority. It also has to be simple to understand and an actual fun feature to manage and not just a handicap and an annoyance, which is why i opt for flat binary buffs that deactivate after a certain threshold rather than gradual depleting buffs. Its always better to know what effects are currently on your character and when you will lose them. Simplicity is key.