I have a nasty suspicion that Karlach's under represented story is because of her late addition to the game. Yes she was in EA but the other Origins had years and plenty of feedback to be fine tuned and reworked. Not to mention how early her story can end due to Wyll. Hopefully patches will arrive enabling us to give our girl a slightly better ending than what we have now.
They had Astarion from start to finish, yet he got the same treatment. Neither of his endings are what he wanted or particularly desirable. The book of thay was a meaningless red herring and all that talk about drinking Cazador's blood was a lie. They set these paths up and then made them go nowhere. Hell, Gale's redemption to mystra is
suicide
. You can tell SH and Lae'Zel were Larian's favourites.