It`s easier for the authors to stuff Janeway into the fridge than Chakotay. This way they don`t have to deal with a female captain unless it`s one that they put in place (Ro, Ezri).
Have you actually read the books? Janeway was replaced with a female captain, Afsarah Eden.
Female characters usually get the short end of the stick unless they`re the star of the show like Buffy, etc. In an larger group, even though one or two characters may be more like a traditional leading character, women usually end up on the losing end as time goes on.
Not in Trek Lit. We have tons of central female characters. Kira has been the commander of DS9 since the start of the post-finale novels. Ezri Dax is captain of the Aventine
now. In SCE/Corps of Engineers
, Sonya Gomez was the commander of the SCE team and the lead character of the series. The Destiny
trilogy focused largely on Captain Erika Hernandez of the Columbia
. The current command crew of the Enterprise
in the post-Nemesis
TNG novels is mostly female. Over on Titan
, Captain Riker's chief advisors -- his first officer and his wife/diplomatic officer -- are both female, and so is his science officer. And the current President of the United Federation of Planets in the novels, one of the most popular recurring characters in the line, is a woman.