First of all, did you ever attempt to use the Honey to catch Pokémon? If not, was it due to the waiting times, lack of species available or something different entirely?
No, I never used Honey to get any poke mainly because I don't like those pokes much.
How do you think it compares to other methods of wild encounters such as Headbutting Trees in G/S/HG/SS?
Headbutting trees was a lot easier than through Honey. So I think this feature Shucks....!
Would you like to see this mechanic return in future games?
I vote for this feature to never comeback
And finally, how the hell does a Heracross fit in a tree?
Probably just sleeping on a Tree Top or something and then fells down when someone Headbutt's it.