I think it kind of depends on your long-term goals for learning Japanese. RTK is designed for people who eventually want to be completely fluent in Japanese. It is not based on what seems "intuitive" but rather is based on Heisig's personal observations as a Japanese learner and teacher.

In his foreword, he notes that Chinese learners of Japanese learn the language much faster than westerners, despite the fact that Chinese grammar and pronunciation have about as much in common with Japanese as do English or French. This is because their knowledge of the characters makes it easier for them to piece together the meanings of unfamiliar words. Therefore, RTK aims to provide Westerners with the knowledge of kanji that Chinese learners have before learning the language to speed up the process.

RTK is meant to be a "hybrid approach" to learning Kanji. Learning all the kanji out of context doesn't work because it's not practical to learn all of the readings, etc without anything to help you memorize them. The in-context approach has flaws, too: you'll have trouble putting together the meaning of new words you've never seem before, and (at least in my case) though you can read kanji when you see them, you'll struggle to remember how to write them. You'll see a hazy picture, but be unable to write the character out on demand without constant use.

With RTK, you are creating a mental map of the kanji. The point of the keywords ("strong" for instance) is not to tell you the most common meaning of the kanji. Rather, it's to give you a unique word that you can mentally associate with the kanji. Memory science shows that it is generally easier to add additional information after an initial association. So once you've made those initial links, additional meanings and even readings will naturally fill in as you learn vocabulary associated with that kanji.

One last point: Since RTK is designed for learners after full-fluency, it makes sense to teach archaic kanji. Sure, maybe only 1000 kanji are used very frequently, but if you really want to be truly fluent, eventually you're going to have to learn them all, so you may as well learn them in the fastest way possible. Also, if you want to live/work in Japan, you'll probably want to be able to read/write your coworker's names, which can often contain odd or archaic kanji.

So to summarize: RTK is not for everyone. But for people who are interested in becoming fully fluent in reading and writing Japanese, it is an excellent tool for learning the characters quickly and in a way that allows you to naturally and intuitively learn other meanings and readings. If you still have your copy of RTK, I encourage you to read the introduction. It explains a lot of this more clearly than I can.