For both adventure paths, once you start deck 3 you remove any banished basic banes from the game. You have the option of doing the same with boons. Once you start deck 5, you do the same for cards with the elite trait.
My group pretty much removes all basic boons except for the following:
1. Cure spell. We keep this around because it's always useful to pick up during a scenario.
2. Easy to pick up allies that give an explore. Keeping these around helps get through location decks faster.
3. Potion of Glibness. In our S&S game, this item has come in handy too many times for us to remove it from the game.
So far we haven't had to make a decision on Masterwork Tools, but I think we may end up holding on to this card as well.