CUSTOMIZE THE "BOX"
With all the cards coming from chests (and future class decks, etc etc etc), it would be nice if there was a way to customize your own "box". For example, remove a Troubadour and replace it with a Smith, or replace all Blessings of Desna with Favors of Pharasma. Or just remove all Longbows if you're playing without ranged-weapon-proficient characters. Maybe go the other way entirely; make the good cards less common so they're more exciting to find. Even just a way to prevent selected Treasure Chest cards from appearing in the game without having to salvage them.
And in the future, with other Adventure Paths, mixing pieces of all the decks together for a really wild ride.
Tweaking the box would be a really fun feature to play with.