It's nothing to do with her gender for me. Troi is not and would not claim to be an experienced command officer. She had no idea what she was doing in "Disaster" and relied on a junior officer (Ro) and a non-com (O'Brien) to help her.
I found it bizarre that Data never made it past Lieutenant Commander in his lifetime. He served in Starfleet for over three decades, risked his life on numerous occasions to save his ship and his crewmates and proved himself to be a capable leader. Worf may have had his disciplinary problems but he was also a very experienced combat officer. Ultimately experience is what matters on the bridge of a Starship.
That is why, when it came to it in "Gambit", Data chose Worf as his first officer - not Troi, Beverly or Geordi.
Troi took an exam and did a few shifts on the bridge in the big chair. That does not make her an experienced field commander. She chose a non-command career path, as did Beverely.
At no point when watching Star Trek did I ever think that Kira or Dax or Janeway lacked authority because of their gender. If anything, the writers portrayed them as trying too hard when the audience didn't need them to.
In that case, it's unlikely that a major dept. head like a CMO or ChEng would be assigned such a position. Their primary duties are complicated enough and may require extended periods of their full attention.
