KanjiTown sounds interesting. I may very well try it out. That stupid AKUmulator story got stuck in my head after me briefly reading it.
I started RTK2 on January 1 of this year, and so far I've gotten to the end of Chapter 6. I gave up trying to memorize every single exemplary compound at Chapter 1. It was far too time-consuming for me, and I got nowhere. Furthermore, many of the compounds is are rather obscure and uncommonly used.
I have found that RTK2's method works very well for me. So far, at least. I'm starting to get a little bit annoyed with the constant work of incoporating new Kanji into my brain, and the exceptions are starting to anoy me. Now that I've gotten out of the pure signal primitives area, I might try KanjiTown. It sounds intriguing and fun.
I will say that RTK2 is a good, solid method, but, like RTK1, you have to stick at it, and it can get very frustrating at times. I know from experience. I got very frustrated with RTK1 on several occasions, almost to the point of giving up, but I never did. I finished it in about 7 months. With a 95% retention rate, I feel quite proud of my accomplishment in that area.
However, you need to read Japanese and use the readings that you learn daily. No amount of mneumonics is going to help you if you can't use the stuff you've learned in everyday life. I read Japanese blogs, translate Japanese, and go through things like that on a daily basis, and it really helps. The readings that I use and see regularly are the ones I remember clearly, while ones like 慈 and others, which aren't used regularly, I remember less clearly. Review past readings regularly, as well. It's amazing how much a reading sticks in your mind once you see it outside RTK2, like on a computer or a Japanese TV show. That alone can force the reading into long-term memory permanently.
Also, don't become dependent on the RTK2 compounds. You need to use the readings in different compounds in different positions, otherwise you'll be learning to read the compound instead of the Kanji. There are certain places where this is totally acceptable and encouraged (明日 is a very good example.

), but most of the time it's not. Like I said, practice, practice, practice.