Through genetics (evolution, family tree, etc), your body has a certain homeostasis. This is for whatever reason(s) what your body has come to believe is the right way to be, so breaking what your bodies nature is, is not going to be easy (of course this rule varies widely).
If it were so simple as plugging yourself into a serial port and laying out what you consider the perfect, ideal human body, then life would be much different. "Eat what I want, when I want, as much as I want, and yet still turn this Hershey's bar into protein and make it build muscle."
Some people are skinny, some muscular, some fat, and most of us are somewhat of a mix of these body types (endo, meso, ectomorphic). If nature could be so perfect on its own to program an aligator to run 75 miles an hour and not tire so quickly as it does when it runs quickly, be impervious to bullets or all kinds of attacks, and be able to go for months without eating, well heck it would be quite the monster wouldn't it - but nature is trial and error, and you just end up with whatever you get from your "grab bag."
Picture the adaptation of a marathoner versus a 340 pound "freak" bodybuilder. Nature will not allow, at least as of yet, a 340 pound bodybuilder to run a 4 minute mile for 26 straight miles, its outside of our abilities as of now. They also said though that the 4 minute mile itself was impossible to break, and science "proved" it too. Each one of them reaches a point where they are good at doing one thing, and not much of the other, just as they have a hard time improving further at what they enjoy doing after a certain point.
The body can adjust hormonal levels, metabolism, all based on your input as well as genetics.