I suggested this to my wife and she thought it was a good idea. We play with all of the expansions, which means that we have 483 Adventure Cards in play. This means that some of our favorite items (for me, the Runesword; for her, the Maiden and the Unicorn) almost never show up.
We are going to try separating some of those cards out into a separate deck. Then when we trade in trophy points we can choose either to take a strength/craft bonus OR draw from that other deck.
I'm thinking we'll make it that you have to trade in ten trophy points to draw from the deck.
I'm not sure what my favorite item(s) would be but like you, it seems, I only play with my wife and the incredible large deck means some things are rare. On the other hand I have noticed that whenever we add a new expansion's Adventure cards to the deck they take a long time to "un-clump" the tendency for them to want to stay close to, say, other Blood Moon cards, for example, which means you could end up encountering long streaks of just those sets' cards.
Like yourself I've thought of ways around that. No matter how differently I try to shuffle and integrate, some will always run in packs, even Frostmarch cards. Probably just need to play more < 'bout once a month >.
Two ideas; which we haven't tried yet. 1) Separate into 2 Adventure decks. Draw 1 for Day and 1 for Night. (not crazy about this one)
2) 3 approximate sized decks. It is your choice which to pick from; every turn you could pick a different one if you want.
this one, is… maybe. I would almost tweak it and say, choose any deck - but no Fate re-rolls on any encounters, since you've already altered Fate by choosing from 1 of 3 piles.