I kind of posted about this in another thread, but I think it's worth discussing generally. I'm wondering why there isn't very much speculation about custom encounter decks, as this (to me) is one of the biggest draws of this game. I think this is an important part of the LOTR LCG, because it abolishes traditional ideas about 'balance' in a card game. IMO, the replay will come from constantly tweaking not only the player decks, but also the encounter decks. Especially those who have their copies already, how might this work? Could you build a custom encounter deck that actually has a specific strategy? Are their limitations? Etc...
Customizing the Encounter Deck
There is nothing stopping you tweaking the deck if you wish or even just putting all the different cards together.
As more sets come out and more options are available for Encounter decks or Quest decks, I can see modifying them to tell a part of the story you want to play through. No reason you couldn't do that if you're just playing at home.