iPhone 5s capacity shows 11.9 gb but they told m 16gb started capacity

That is correct on the usable storage after you subtract what is used by the apps and iOS.

Not to mention that "16 GB" is never truly 16 GB on any storage medium due to decimal vs. binary counting. Even a 16 GB USB stick is 14.8 GB at best.

Me too! Then i have one more problem! I go to manage storage then it's shows only 1.5gb left but i compute my apps i used only 7gb !!! And my memory is 11,9 , where is the 3gb!????