Irreducible Complexity.

[leo-rcc]

Snakes have lungs, snakes breath air, they just don't have a diaphragm (so no hick-ups) and no larynx. Their mode of transportation or circulatory system is not the subject at hand, but the respiratory system is, so how they move or look is not relevant in this case. So my question stands, why is it other animals that do have their airways and food intake separate have none of the issues described above? Why couldn't it have been done any other way?

As for mammals, most if not all have a Larynx, since mammals have common ancestry, the trait of having a Larynx is passed down from generation to generation.

Evolutionary opportunism results in suboptimal functions and structures. In gradually evolving a new function, organisms must make do with what they already have. Thus, functions are likely to be performed by structures that would have been arranged differently (e.g. more efficiently) if the final function were known from the outset. "Suboptimality" does not mean that a structure functions poorly. It simply means that a structure with a more efficient design (usually with less superfluous complexity), could perform the same final function equally well. Suboptimal structures and functions should have a gradualistic, historical evolutionary explanation, based on the opportunistic recruitment of ancestral structures, if this history is known from other evidence (e.g. if this history is phylogenetically determined by closely related organisms or fossil history).

The mammalian gastrointestinal tract crosses the respiratory system. Functionally, this is suboptimal; it would be beneficial if we could breathe and swallow simultaneously. Unfortunately, we cannot, and this is why we are susceptible to death by choking. However, there is a good historical evolutionary reason for this arrangement. The Osteolepiformes (Devonian lungfish), from which mammals evolved, swallowed air to breathe. Only later did the ancestors of mammals recruit the olfactory nares of fish for the function of breathing on land. It so happens that the nares (originally used only for smelling) are on the opposite side of the esophagus from the lungs (Futuyma 1998, p. 5). Mammals and therefore indeed humans have inherited this original design, even though it now causes problems.

Ref:
29+ Evidences for Macroevolution Part 3: Opportunism and Evolutionary Constraint by Douglas Theobald.
Futuyma, D. (1998) Evolutionary Biology. Third edition. Sunderland, MA, Sinauer Associates ISBN 0878931899, 9780878931897.