Heisig’s method focuses only on you learning the writing and rough meaning of each character. While it may seem that not working on the Japanese/Chinese readings renders Heisig’s method incomplete or even useless to some people, the method focuses exclusively on the recognition and writing of the kanji/hanzi for a very specific and important reason.
In a nutshell, through Heisig’s method you gain the same advantage that a Chinese person would have for learning Japanese from scratch, or viceversa:
People from China/Japan are already familiar with most kanji/hanzi characters, and relate each one of them to a certain concept in their own language.
Thus, already knowing how each kanji/hanzi looks like, and what they mean, they only need to learn how to read them in the other language they want to learn.
Flashcard structure ideas for learning logographic languages.
This may sound like a terrible generalization but the Japanese language has taught me that a person’s understanding of the world need not be so well articulated — so rationally articulated — the way it tends to be in Western languages. The Japanese language has the full potential to be logical and analytical, but it seems to me that it isn’t its real business to be that way. At least, not the Japanese language we still use today. You can mix the present and the past tense. You don’t have to specify whether something is singular or plural. You aren’t always looking for a cogent progression of sentences; conjunctions such as “but,” “and,” and “so” are hence not all that important. Many Japanese people used to criticize their language for inhibiting rational thought. It was quite liberating to me when I realized that we can understand the world in different ways depending on the language we use. There isn’t a right way or a wrong way.