Fred and Wes had been building for 2 years up until that point. They had a mutual intelligence thing going on before the betrayal. And even after Wes’s betrayal, Fred still tried to go to him when needed. And in season 4, they seemed to get along a lot more, which bled into season 5. The writers tried to throw it with the Knox thing, but there’s always been a little something between them.
Personally I have always felt Fred and Gunn seemed more out there as far as chemistry and connection went. I like Gunn and Gwen a lot better. They had that same streetwise energy going on that really worked
Other than toughness, Gunn and Gwen have little in common. Gunn is a social person, connected and protective of others. He is warm, friendly, caring and involved. He is smart and resourceful, as is she. She is also utterly calculating, ruthless, self protective and cold to the point of being dangerous -- not just because of her condition, but that doesn't help. It isolates her and Gunn gives her a moment of respite, but she will always be about 'Ms. Number One'. Gunn will always be about the group -- his sister, his gang of street protectors, the AI group. There is no place in Gwen's life for 'joining' or being part of.
For Gwen, you get the feeling that connecting with someone was something that happened to other people. I don't see any way she was going to become a team member. She would not have fitted into Gunn's life as other than a fling.
Fred and Charles are both working class kids who don't have airs or graces or 'big ideas' of how 'cool' or 'important' they are. They work well together and they work well with others. They are confident in their abilities and those abilities compliment each other. Fred is not a high brow person; neither is Charles. Notice that Fred sees him from day one... she sees 'Charles' NOT the 'street fighting caricature' that he could have been (and sometimes almost becomes in the series). They became friends. They enjoyed trips to the diner. They made each other laugh.
For me laughter is always fundamental to a good relationship and a good marriage. If you cannot make each other giggle, then you've got vapourware. (the kind of software that promises lots of wonderful things but never delivers).
When Connor was a mess, they did their best to take care of him. They even seemed to succeed to a degree. Though I think Fred was absolutely wrong to taze him after finding out what he'd done to Angel, I think part of it was a sense of betrayal. She'd LOVED him and tried to raise him. But even good parents make horrible mistakes. She was a young woman trying to parent an out of control stranger.
I can see Fred and Charles 30 years from now with their grand children, laughing and playing on the floor. One of their sons went to Caltech, one of their daughters went to Harvard law. Both are black belts. Both of them like making stuff. Their family home is a relaxed one. The elderly Burkles have an in law apartment on the ground floor. All friends are welcome.
I cannot for the life of me imagine Wes and Fred's house together. Or joy or laughter. Maybe the two of them in velvet high back chairs sitting in front of a fire, their heads in separate books. No conversation. No kids. No laughter.