I believe that a serious study of kanji (such as Heisig) is best left for a more advanced level of Japanese. Beginners often overload themselves trying to learn thousands of kanji when they don't even know the meanings of the compounds that the kanji are used in. I believe that Heisig even mentions in his introduction something to the effect that using his book won't really improve your Japanese, it will just improve your ability to learn Japanese. Rather than spend hours per day studying Heisig for months, I would recommend a more traditional approach to beginners of learning the most common kanji as they learn the vocabulary.

For the advanced student looking to master kanji, then a method like Heisig's seems best. However, for those interested in the Heisig method, I recommend this book: Kanji ABC [1]. It is similar to Heisig's but organizes the kanji so that you learn similar kanji together. Also, while Heisig spends much time trying to get you to memorize convoluted association sentences, Kanji ABC simply gives you the radicals (similar to Heisig's 'primitives') and you build your own association sentences.

[1] http://www.amazon.com/Kanji-ABC-Systematic-Approach-Characte...