Bones is done great and I hope to see him in another game again, doesn't have to be new Risen.
Not sure for the rest of those guys because I didn't use any of them extensively. On replay since I'll go early with healing and take Edward to see his story.
Dull or not, Patty (even in this botoxed version) and Bones are memorable characters just like Diego, Gorn and Milten were. That *is* the strength of PB games.
EDIT:
One thing just so you know. If you'll go on positive soul value, make sure you solve two Mendoza pirate captains dreamquests before having him on your ship!
There are IIRC 6 of those quests, but two are not possible to solve if he's gone (Steelbeard from JDR's easteregg thread and that other pirate captain I can't remember his name). For whatever reason, you can't pickpocket or duel/loot necessary items from NPCs in these quests (unlike for example Taranis' warehouse master who's key you can get by smashing him and looting even before Patty finds out about his chest).
Other four you can solve even if he's gone because you'll find necessary items during your exploration, but those souls are not of pirate captains.