If I had to choose, I'd just do RTK2 using Anki. Instead of using kanji chains or memory palaces, I'd make it much easier on my brain and my free time. I'd take each vocabulary word he introduces as an example of an on-yomi, find an example sentence in a dictionary or other verified Good Pile of Japanese Sentences I Trust, and then stick that in my Anki deck, with recognition and production cards. (So a card where I read the sentence with the target kanji in it and have to get the reading right, and a card where the target kanji is in kana, and I have to write the kanji correctly.)
Sort of like this:
for 義 he has 義理 (ぎり)
Reading:
Q:友人に義理を立てる
A: ゆうじんにぎりをたてる
(do one's duty by a friend)
Production:
Q:ゆうじんにぎりをたてる
A:友人に義理を立てる
You can add or subtract as many kanji as you need from the production side. A lot of people just target the the one kanji they're working on, because it can get slow otherwise. I just grabbed this phrase off of the Yahoo dictionary, but you can use whatever source you want. It doesn't even have to be a full sentence, really.
I suppose memory palaces can be really efficient, but rather than spend all that time building another artificial memory construct on top of RTK1, I'd rather spend the time putting sentences in my deck. (Because I'm lazy.) Also, the sentences will give you a better sense of context than studying the words in isolation.
I haven't had much luck with Anki cards of just isolated words. I tend to flunk those a lot, because there are so many homonyms in Japanese. I can't tell if けいたい is 形態 or 携帯. Bah. So I use sentences or phrases.
You'll still get the benefit of the associations of the various groups as you learn them, but to be honest, I'm not so sure that the signal primitives are always that helpful. Sometimes I get confused by 性 and 生 in certain words, as well as 製 and 制 in certain others... and yeah, they're all read せい. Okay, they're helpful for reading, but not always for writing. I should be clearer on that.
That said, I think it's all a question of what suits you best. To be honest, this is all nitpicking on everyone's part. Everyone on this message board has their own individual learning preferences, and they won't hesitate to state them.
I like the path of least resistance, and that which requires the least amount of effort on my part. I don't want to have to think too much after a long day, so I don't want to sit there and try to squeeze out the contents of an entire palace to remember a word. I'd rather just train my brain so it sits as close to my brain stem as possible, and give myself electric shocks until I remember it. (No, not really.)
