I don't seem to have much of a problem with energy loss with my character. I have pretty high strength and agility and fortitude and can seem to run a pretty far distance and stay over 1/2 most of the time. I can sprint pretty far also and this is with starting skill in running. I think I've gained maybe 3 points in running so far as I've been swimmimng alot.

As for swimming it does seem like you should drown if you run out of stamina completely. Maybe have a type of rest action for the water where you float on your back to regain stamina. but you would be floating with the current (if thats ever introduced).

I don't know how well that'd work but it just seems like there needs to be some disadvantage to running your stam to 0 in the water.