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?
Yes. And failed, as I didn't understand it (Either didn't use enough honey or didn't come back soon enoguh / came back too soon). Eventually did use it, never found a Munchlax or Heracross though.
How do you think it compares to other methods of wild encounters such as Headbutting Trees in G/S/HG/SS?
Headbutt was way superior. Even without the tutor, it would still be more practical as you don't have to take it all seriously and concentrate on your timing (i.e. coming back at the right time), and it doesn't cost money.
Would you like to see this mechanic return in future games?
No. a) it's a bit rubbish and b) it should be kept Sinnoh-exclusive as some things have been kept exclusive to other regions (such as Headbutt, lack of berries in Kanto / Johto etc.).
And finally, how the hell does a Heracross fit in a tree?
Where the hell does your mom sleep when you have the only bed? Why do the bad guys just give up instead of using Revives and attacking you personally with their pokémon as opposed to battling? Why does Barry's mom not know who he takes after? (Well, we all know that one hehe -_-).
Just accept it. Although my reasoning would be that trees, like houses, are bigger on the inside, because they're all Tardises, or Tardi, or Tardis' or whatever than they appear when compared to the player. And you put honey there, so Heracross will find a way, any way, even if it means killing so many Wurmple the tree turns yellow with their decaying corpses.
Sorry, got a bit morbid there. But Spain just got there arsses handed to them by a team who drew with England a month ago so, you know, anarchy, end of the world and all that xD