The first season, Jane was more of a Tom boy, and her toughness added realism to the show. It contrasted with the hyper-feminine Dr. Isles and made the show more interesting.
Bringing her brother too quickly to the homicide unit also felt weird.
Each season of this feels like an entirely different show, and viewers have noticed. Ratings have gone down every season. In season three, the writing is predictable and seems to be modeled off of every other female lead crime show from the late 90s and early 2000s. Before, it felt fresh and more interesting.
It seems the writers/network were afraid of the lesbian fanfic and ruined the show. Maybe instead they should have listened to the ratings and stood their ground.