It’s easy to forget that languages are a product of thousands of years of evolution. A quick look at historical linguistics can give a language learner some perspective on their target language. I’d argue that there are few truly vestigial structures in modern languages.
In linguistics, as in biology, the overall system is so complex that it’s difficult to label a structure as unnecessary. A sense of humility ought to imbue us; we now know that we were wrong about the vestigial nature of the spleen and appendix. We deem things useless when we don’t understand them. I’ve heard the same thing over and over in the classroom about articles, strong verbs or the tense-aspect-mood system in English. The thing is, articles and the sequence of tenses are relatively new in English. Much to the chagrin of linguistic Platonists, languages are becoming vastly more complex over time rather than being dumbed down.
When confronted by the complexity of a language, be awed by it. Ask yourself what function it serves: articles quickly add clarity about the something’s level of abstraction; Japanese honorifics weave culture into the fabric of the language. If something escapes an obvious explanation, it could very well mean that we don’t understand it well enough.
Have some fun researching the history of whatever language you are studying and try to think why that language community evolved the way it did. Thousands of years of linguistic evolution have produced our modern languages, let’s not be too rash in forgetting this.