This is the sort of discussion I was hoping for. I only tried rote memorisation for about a week and was getting pretty frustrated, until somebody introduced me to Heisig on here, so it's interesting to learn a little bit about alternative approaches. Before I tried the book, I read about the 'story' technique randomly in an article online, and thought it sounded stupid and unnecessary, and never gave it a second look. After getting about 300 characters into the book, I felt I was making good progress, but wasn't really creating the vivid images Heisig kept talking about.
Perhaps the biggest flaw with the book is Heisig stories, which stretch for the first 600 or so characters. These mnemonics need to be unique to the individual to work effectively. I found it started working almost perfectly when I ignored Heisig's version, and just started going with the first thing that came into my mind. As English speakers, we already have image associations for most of the keywords, a strong mental link - the crux of the method - which can be immediately utilised. In these cases, even imagination isn't necessary.
Like Belton was suggesting, I think after 3-4 years, there might not be too much to separate the two methods. Of course, there are so many variables between two given students studies that it's practically impossible to quantify. Nevertheless, if a guy can read a newspaper and write a letter 4 years in, how he gets there is purely a matter of taste. Among many other things, I liked having the intimidating aspect of kanji taken away early on, with what I felt was minimal effort, and then being able to try reading/anki'ing what I pleased, without being concerned with sticking to Level X. Others may prefer teachers, structure, and whatever else, but I think keeping an open mind and at least giving new things a try is always a good thing.
