When using two tiers of location to remember kanji, it becomes easy to learn them independent of each other while still maintaining the advantage of location based learning. The first location, the movie, is what allows the grouping of kanji by onyomi. The second location, the scene chosen within the movie based on character meaning, is a completely new innovation that allows kanji to maintain independence from each other while making it possible learn the onyomi and the kanji together.
The three most well known methods for remembering the onyomi are the Kanjichain method, the Kanji-town method, and James Heisig's second book Remembering the Kanji II. I will compare my method with Kanjichain and Remembering the Kanji II only, because Kanji-town is essentially the same as Kanjichain.
Kanjichain, a step in the right direction
The idea of using "chains" to group kanji together was a great idea for many in the community. While the author intended for his method to be implemented to learn the onyomi with the kanji, it was not practical in application. Because of this, there are many people who use the kanjichain methodology after completing Remembering the Kanji.
There are two fundamental differences between my method and the Kanjichain method. These are: location vs. chaining and independence of kanji vs. dependence of kanji. While there is no doubt that using chain associations to group kanji together by onyomi is effective, I do doubt the the overall effectiveness of kanji being dependent on each other. Links can degrade which will lead to the loss of the rest of the chain, it can be time consuming to review kanji that aren't at the beginning of the chain, and it can be difficult to create an effective story that contains all of the necessary elements for kanji. (If anyone would like to comment and give their experiences in chaining or tell me how wrong I am about it, please do.)
By using location extensively, it is no longer impractical to learn the kanji in groups of onyomi, because the location is the only reason I am able to break down kanji into so many components. I'm not trying to remember a list of the components, just a scene. By adding a second tier, the location within the movie, everything "unlocks". It is no longer necessary to maintain a large and bloated mnemonic, and the onyomi are impossible to forget.
Remembering the Kanji II, signal primitives, and Christine_tham
Heisig's infamous second book, Remembering the Kanji, was a total letdown in comparison with this first book. It was entirely a brute force method to memorize the readings. But having never used it, I cannot say how effective or fast it is. It uses "signal primitives" to indicate readings, starting with pure groups that signal a reading, and advancing to groups with more and more exceptions. If you want a crash course in the phonetic components after completing Heisig's first book, this is it.
However, on the topic of phonetic components, I would say that doing my method to learn the kanji will give the ability to read phonetic components normally reserved for natives and scholars. Christine_tham, in the Reviewing the Kanji forums, has stated that one need only learn the first thousand joyo kanji with the ability to guess the readings of the rest. Ignoring the obvious stupidity of this claim, I will counter that I know the entire joyo list with their onyomi readings, and can guess the reading of an unknown character with the same accuracy she claims to have.
With all that said though, phonetic components are only good at reading faster. If you actively study them to the level of knowing EVERY one, it's just insane and won't help much. I already have a decent ability in reading phonetic components after completing this method, so I doubt I'll need to study them much more. But if you want the insane understanding Christine_tham advocates, it would take only a very small amount of extra studying to attain it.
When it comes to learning onyomi after having completed Remembering the Kanji (congratulations to all of you, by the way), I cannot say if my method would be faster than the three methods already out there. It's also important to note that side benefit of learning phonetic components will not apply to people who are not using this method to memorize kanji. While I will say that my method will probably be slightly more reliable for memory, I cannot endorse it for learning the onyomi exclusively unless somebody actually tests it and reports positive results. This is because the deciding factor for learning onyomi after completed Remembering the Kanji is not effectiveness, but speed.
Update: I said before that learning the phonetic components was exclusive to people who used this method for learning the kanji and not just the readings. However now that I think about it, I really can't say for sure. It's possible somebody dedicated could learn the phonetic components after completing RTK and reach the same level as I claim. I would encourage somebody to try and report how it goes.