In my experience, his method just seems to encourage too many naive learners who think that "learning kanji" (learning the characters and what they "mean", in English) is learning Japanese.
The title of the series is
Remebering the Kanji. Your criticism here is as ridiculous as saying dictionaries are bad because they don't teach you compsition skills. Also, it's not a valid argument to say that the method is not effective just because a few stupid people can't grasp the meaning of those three simple words.
Heisig's method is a structured, systematic way of remembering the writing, reading, and usage for 3,000+ kanji. Stop and re-read that sentence a few times and the consider the implications for a moment.
Let me make an analogy to illustrate what I'm trying to say. Say we're both trying to build a 100-story building. You start by thowing some boards and drywall together, while I consult with an architect and prepare to pour the foundation. At first, you might say to me, "Ha! My way is better! Look, I've got 4 floors built and furnished already while you're just dumping cement into a big hole!" However, while the haphazard approach may give you the impression of quick progress at the beginning, you'll soon discover that it falls apart the further you try to take it.
Software development is another good example. The techniques needed to create a million-line program are quite different from those used to create a program with only a few hundred lines. Novice programmers will often find these more advanced abstractions confusing and overly complicated, but without them it would be nearly impossible to write, maintain, and extend large pieces of code.
Similarly, Heisig might seem counterintuitive to the beginner at first, but when you consider the its large-scale goal, its structured, systematic approach begins to make sense.
Don't get me wrong, I'm not knocking rote memorization. Mnemonics and rote are simply different tools that are each suited to different situations, in the same way that each tool on a carpenter's workbench has a specific use.
For example, rote is probably the better method for learning kana. For such a small number of characters it would probably take more amount of time and energy to invent mnemonics than it would to simply memorize them. Rote might even be a better choice if all you want to learn a small number of kanji in the course of a beginner-level class.
However, if the goal is reading, writing and using 2,000-3,000+ kanji, Heisig is simply a much faster and more efficient tool.