The complicated course of the facial nerve is due to it's evolution and embryological development. About 450 million years ago the anterior gill arches of some aquatic vertebrates evolved into jaws and supporting structure. Three of these jaw bones would later evolve into the the 3 middle ear bones that are causing your father's problem.
These structures are all derived from a structure called the 2nd branchial arch in the embryo. Structures that arise together in the embryo are supplied by the same nerve. As those structures become separated during development, the associated nerve follows. Branchial arch 2 also gives rise to the muscles of facial expression -- all the small muscles of the face that blink the eyelids, smile, frown, etc. As these muscles spread out during embryological develop, the facial nerve follows. This results in a complex course of the nerve, including through the middle ear.
That's how evolution works. It doesn't create an optimal design for each species out of nothing. Rather it modifies current parts over time.
By the way, the same thing happens with a nerve called the recurrent laryngeal nerve. This nerve starts in the brain, travels down the neck to the chest, loops around a main artery and then travels back up the neck to the larynx (voice box). This is related to the evolution of the laryngeal muscles, which fish -- not being air breathers -- don't have.
