A good balance can't be done without trial and error, and PoE I went all the long way to version 3.07 so i'm quite optimistic for the future of Deadfire. =)
A good balance makes an OK game a great one. Even for a single-player game it is much needed for replayability – for why bother playing with another build, or class, or watever if you already found the most optimal path to victory. Yes you can chage your behaviour in the game, choice and consequence and stuff, but it is just so much more fun to do it with a complete change of play-style as well. It was done good in PoE I, it killed Tyrany for me (as much Lore as possible and you are well packed). Like, well, as much Alchemy or Arcana... You get the drift.
For the problem of consumables duplicating class abilities – it would be fun if classes and sub-classes had unique interactions with the skills and consumables. Poisons and Assassins, Bombs and Black jackets, Wizards and their scrolls, Corpse-Eaters and some very special foods... they all should have some powerful perks for kinda doing what they are supposed to do.
And Sleight of Hand is usless. As an "active" skill anyways. Just saying.