Honestly, when I first played, I couldn't figure out how honey worked. I had skipped all of what the honey-giving man had said, so it was almost impossible. Deciding it was a glitch, I progressed on with the game. However when I did find out how the honey concept worked, I decided to give it a go but I decided the waiting period was rather long and not worth it at all. I never came back to find any of the rarer Pokemon living up in those trees, since I found it a rather tedious chance. 1% of a chance to find Munchlax and only in four trees- that would take forever. I'd rather breed Snorlax to be honest.
Other than that, I think the concept compared to the other methods was rather creative but also rather irritating having to wait. Sometimes you might not even get a Pokemon and that would be frustrating. I liked the Headbutt method more, since it was simple and quick. I'd rather not see it return in future generations. Although it was creative, I just didn't really like it.
As for how Heracross fits in a tree, I think that's because of something called magic. :]