I've only watched seasons 1 & 2.

Season 1 was cringe and pretty shit because Seth MacFarlane sucks at comedy and he put all his friends on the show instead of hiring actual actors.

Season 2 got considerably better because Seth tried to make a serious TNG-like instead of constantly making fart jokes.

Apparently Season 3 just started.

Here is the "pro tranny" plot summary:

Kelly offers to mentor Topa and help him prepare for the Union Point entrance exam. The two bond and Topa confides in Kelly that he feels there is something wrong with him. Kelly feels that Bortus and Klyden should tell Topa that he was born female but Klyden steadfastly refuses and forbids Topa to continue training with Kelly, which leads Topa to begin having suicidal thoughts. The actions of both Kelly and Bortus lead Topa to the truth of his origins. Topa decides to return to being a female and asks Claire to reverse the gender reassignment surgery. Klyden protests and threatens to leave Bortus but Bortus consents. However, the admiralty refuses to allow the surgery since allowing it would cause Moclus to leave the Union, leaving them vulnerable to the Kaylon. Claire volunteers to resign her commission in order to perform the procedure without causing an interstellar incident but Isaac volunteers to perform the procedure, as he is not officially a Union officer. Ed orders Isaac not to do it but then arranges a concert in the shuttle bay for the crew to give Isaac time for the procedure. Despite an attempt by Klyden to stop the surgery, it is successful and Topa is restored to her female form. Klyden furiously renounces his ties with Bortus and Topa but Bortus reaffirms his love for his daughter and Kelly resumes mentoring her.

How is this pro-tranny? The plot is about Topa DE-TRANSITIONING. It's about as anti-tranny as you can get, especially anti-transing children.