I can't see any other reason than that they did not anticipate Karlach's popularity (which is mostly due to her voice acting, no?) and thought she'd be just fine with her current, limited and very railroaded "story arc". But as she turned out to be one of the most popular ones, they have a decision to make.
Karlach is popular because of multiple factors (not exhaustive and in no particular order):
Looks:
1) She looks cool. 2) She's an attractive woman. 3) She's a buff girl -- all the rage these days, 4) She resembles a demon -- a very enticing and popular archetype.
Personality:
1) She's very personable. 2) She's vibrant, upbeat, and endearing. 3) She's a tomboy -- all the rage these days. 4) She has cool, memorable lines.
Sam made a lot of the above happen. She started off quite different from how she ended up. Larian was probably aiming for her to be popular, given the intentional reworkings of her design and personality, but didn't have enough time to flesh her out.
