Sorry, but this made me chuckle a bit.
The vocab they choose is (mostly) chosen for a specific reason, which has to do with the Jōyō and other commonly used words in Japan. You might think you don’t need some random word, but, again, since these are the most commonly used ones, I’m at a loss to figure out why you wouldn’t want to learn them. There are a lot of advantages I can see to learning as many common words as possible.
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Reinforcement: learning words that are in other words reinforces both. (In your example, やまびこ, reinforces 山.)
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Language is dynamic: You say “I don’t need these.” How could you know that? Language isn’t that straightforward. With simple systems, maybe you could configure and tweak things a certain way, but it would be extremely hard to predict the course of a conversation or what you will or won’t see in a book or show or what have you.
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Why not?: I don’t really understand why you’re using this application if you want to pick and choose a very specific set of words. At your level, you’re a paid member. If you want ONLY certain words, why not save your cash and use a normal flashcard app? In terms of time, there’s not a massive time cost in learning each word, and, as I mentioned above, the more words you know, the more prepped you are for reading, listening, etc. So… why not just learn the word?
I guess at the end of the day, it seems like a weird complaint to say the app is teaching you too much. I could understand if it was teaching completely obscure words, but I don’t think “echo” is that weird a choice.