I can argue back that each of the two discrete pathways would be narrower than the one common pathway we have, so having a common pathway is not as stupid as you are making it out to be. This answer is poor because the risk of choking is much more problematic than having a narrower airway.

Earthquakes are also mildly useful in that they bring out precious metals to the surface of the earth. I am pretty sure an omnipotent god could have brought out such materials without having to kill millions of people each time he did it.

Regarding the appendix, I frankly don't care if a handful of doctors claimed the appendix had some trivial functions. The way I see it: people without an appendix are indistinguishable health-wise from people with an appendix, while until a very recent time, people with an appendix had to worry about dying when it inflames and ruptures. Humanity would have been much better off without an appendix.