I think Nintendo noticed a crucial aspect or something (we do not) during the early stages of Skyward Sword, 'ya know? Perhaps it was absolutely necessary for a stamina meter to be implemented. It might have something to do with the motion controls, and how deep and involving they are this time...
I agree with Azure as well. They should allow you to increase your stamina over time, though.
The increase in stamina might break into the realm of an RPG, which could be a double-edge sword, as many might would disapprove...as oddly as it seems...so yeah.