Knocking your head on the wall of realism is not a solution. OK, in real life I'm unable to run with my after-school snack. Not too serious cause I don't go to school any more!
As for every disappointing gameplays, cheaters and even adult scripters find solutions to bypass these points. It takes few time to have your own addon and no more problem with fatigue/stamina, even if some servers kick you (not so much).
The problem is: how BI can satisfy most of players, avoiding such bastard solutions?
What about home made (but great mods) with plenty of magical equipments (extra-huge backpacks, light weight machine guns with Uranium bullets, light but super-efficient armored vests...?
The answers are:
1 - a charter for "compatible" or "BI consistent" addons which complies to the vanilla statements (equivalence in weight, armor, capacity, velocity, power)..
Scripters should declare to be compliant with this charter (something like signature for addons);
2 - Difficulty settings, BI in charge of that point...