Dishonored 2 now has a New Game Plus mode allowing you to continue powering up your character (or characters) on a subsequent playthrough. Yay! But it's not that simple, as some things don't carry over. Here's what you should know before beginning:
Unspent Runes don't carry over. Neither do unspent whalebones, coins, or Bonecharms.
As such, you'll probably want to invest in the Bonecharm Crafting perk late in the game and upgrade it to Craft Runes. Then, before completing the game, you'll want to break down every Bonecharm you have and use your bounty of whalebones on crafting Runes. As mentioned above, you can't take it with you, so spend, spend, spend!
There's only one problem: Attaining the Rune Crafting perk costs a whopping nine Rune to upgrade to. Should your late-game save not have enough Runes left, don't despair! Crafting Runes costs a lot of whalebone, (nine per Rune) so even if you're diligent about collecting these and break down all your Bonecharms, you'll still only net enough to gain a few extra Runes.
Should you not be able to afford Rune Crafting you should still opt for the Bonecharm Crafting perk, which only costs a single Rune, then break down every Bonecharm in your inventory before rolling the end credits because the various traits you get from doing this will carry over into New Game Plus, even if the Bonecharms themselves will not. As such, you'll be able to craft new Bonecharms just as good as the old ones (once you gain enough whalebone anyway).
Despite these unexpected, cumbersome limitations, the good news is that once spent, all your Runes will not only carry over, but you'll be able to re-spec all powers once you hit chapter two. You'll also keep any blueprints you unlocked at the Black Market.
Furthermore, you'll gain access to all powers by both characters, regardless of who you choose. So if you wish to play as Emily again but want to try Corvo's powers, you needn't switch characters.