Both points in reply are true, but he's bang on about the cop-out ending to Desdemona and Samson's story, and about the dismal ending to Ebenezer's story.
Particularly because of the strong opening and mid-story of both these side quests, which makes the endings' failures stand out. Simple endings that aren't so facile aren't hard to conceive of.
For example, you could choose to argue for Desdemona to forgive Samson. If you win RPS, she's still too angry to listen, at which point she leaves. Then after some time passage, she could decide to forgive him later - they could come to tell you about it, or you could have to return to the lighthouse to find that out. Hell, you could go back to the wreck at Black Cove and argue some more, but that's maybe more than the side quest is worth.
Alternatively, you could argue for her not to forgive him, win RPS against him, and have her leave him there in his own personal hell.
For Ebenezer, it shouldn't be hard to script a conversation where you confront him with what you learned from Sam. Either you win RPS: he slips up, they kick his ass, send him to his punishment and move on themselves - or you lose RPS: and the ghosts attack you much as they do now.
Alternatively, he could bribe you not to tell what you learned with partial info about the chests buried in the graveyard. You don't actually gain anything other than character traits, but there's nothing new to code either - all of those suggestions use mechanisms already in the game.
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I haven't followed the conversational path yet where you agree with Jahan about his precious necromancy, but I don't imagine that would sit well with Madora. There don't seem to be a lot of consequences active yet for disagreeing with the henchmen.
