Going to respond to mostly specific statements here, Ruby.
Regarding B'Elanna Torres, she is an incredibly talented engineer. B'Elanna is also important for me because she's one of the rare instances where someone in Star Trek isn't an acceptable form of alien or human. You see it here in the language you use as well when you describe Klingons as "insane." They're not insane. They have a very structured culture with very clear rules regarding their behavior.
B'Elanna's issues stem from her feelings of abandonment by the father that wanted her to find her own way in life and the mother that married a human but wanted B'Elanna to behave like a Klingon exclusively. This is something that mixed children must struggle with throughout their lives. Janeway puts B'Elanna in a position of authority and she rises to it and handles herself well, and over the course of the show we get to see B'Elanna deal with crippling depression about the Maquis and her constant identity issues.
This is probably my favorite scene dealing directly with B'Elanna's struggles with her sense of identity .
Regarding Janeway, I am okay with the decision to trap them in the Delta Quadrant. How many times have you seen Kirk and Picard doing the right thing and they're magically back to where they started by the end of the episode and we just chuckle about it? Janeway's determination to follow Starfleet protocol was probably the hardest and probably the smartest decision she made as captain. Federation ideals trapped them in the Delta Quadrant, and she was determined to have them get them out as well. Without sticking to them, it would become all about Janeway's ego and not about the uniform they represent.
Regarding Neelix, I've never gotten over the grossness of his relationship with Kes and the way he constantly trolls Tuvok and refuses to use his name. For someone claiming to be an ambassador, he is not polite to Tuvok.
Regarding the Bajorans, they are one of my favorite species introduced into Star Trek. Setting DS9 near Bajor meant that we got to see daily interactions with a deeply religious people and see how they lived. You cannot cover the way religion impacts people's lives in a single episode, so seeing seven seasons of the Bajorans allows the viewer to explore a religious people in the very non-religious context of Starfleet. Additionally, these people have suffered tremendously and we get to see how that impacts as people. When you're dealing with a Bajoran, you're seeing someone who's been traumatized their entire life and shares that trauma with everyone they love and know. That's deeply affecting and well-handled by the show. That plays into Bajoran politics. All of these people are survivors and they're all headstrong because of it. Each of them survived the Occupation in various ways and were used to operating independently. That just doesn't go away now that the threat has seemingly passed.
Regarding Sisko, he states multiple times that he is not Picard. He himself was very uncomfortable with the role of Emissary, but every time he leans into it, everyone around him from Starfleet comments on how uncomfortable it makes them. However, each time he leans into it there's a benefit for everyone. Telling Bajor not to join the Federation when they did save them from the initial wave of the Dominion and kept Bajor in a position to do what they do best: guerilla warfare. Sure the show ends with a final confrontation regarding the Prophets and the Pah-wraiths, but this comes after Sisko successfully helps orchestrate the entire war with Admiral Ross after leading the Defiant crew on multiple successful missions. He never stopped being a Starfleet captain. I wrote an essay once explaining how Sisko likely went to the same high school I went to in New Orleans because of his military background and understanding of spirituality.
Interestingly, Avery Brooks was not happy with the end of DS9. He didn't want to become Space Jesus. He didn't want Sisko to leave his family and his son. Avery Brooks only took on the role because of Sisko's positive relationship with his son.
Regarding the Cardassians, I am glad the show hired Marc Alamo to play Dukat, because it's important for people to see the ego and horror of someone like him. The Cardassians violated Bajor for half a century and do not own this fact. One of my favorite confrontations in the show happens between Kira and Damar late in the show when he's horrified at Dominion brutality and Kira claps back, "Yeah, Damar, what kind of a people would harm women and children?" The Cardassians have been awful to their neighbors and love to think of themselves as better than others and that ego leads their entire people to ruin.
Regarding the Ferengi, it sometimes frustrates me with the show how often they're used for silly stuff or "shenanigans" as you've put it. Quark makes a very valid point that the Ferengi haven't been involved in a major war in thousands of years because of their ability to negotiate with everyone.
Regarding Enterprise, 42-minute compared to the previous 45-minute episodes of Star Trek hurt the philosophical aspects of the show. The rugged sticktoitiveness of Enterprise wore thin quickly and I got tired of seeing the command staff constantly captured. I was okay with the premise of seeing the building of the Federation, but I've grown weary of human-centric Star Trek.
Regarding TNG, I do not like that Dr. Crusher and Counselor Troi are relegated to nurturing and advisory positions for the entirety of the show. I do not like how Wesley's relationship to all of the male characters is presented as more important than his to his mother (his surviving parent). At this point, however, I don't end up watching TNG or TOS as much anymore because of its episodic nature. I much prefer engaging with shows with a long-term sense of an arc about where their characters are headed and their motivations for their actions.