Specifically when studying Japanese, I don't necessarily think studying rare words is a bad idea. While many people limit the vocab they learn to a certain frequency list (which is fine), I think there's plenty to gain by doing the opposite.
When Learning Vocabulary via "Chunks" of Kanji, the goal is to build a strong intuition for ~100 kanji before moving on to the next batch. The issue with studying only common words is that you may be forced to move on before building sufficient intuition. Learning less common words can fill in those gaps and get you more comfortable with those kanji, which I think makes future learning in general a lot easier.