Since everyone knows about Karlach and other issues, I am going to mention Dark Urge.

As much as I love this origin, it is very inconsistent, unrewarding and was most likely added last. Sure, it adds to the game plot, but it has got issues.

Commiting to urges is not rewarding, most acts dont matter, you don't gain anything from most of them, etc. Then there are narrative inconsistences in acts 2 and 3, which only sour the experience.