I think the reason Blair and Dan are better friends that Blair and Serena is because Blair/Dan have more in common. If you actually pay attention they have the most intellectual conversations. Not only that, but they are able to kind of tease/make fun of each other knowing that they actually care for one another.
I just always loved the chemistry and the journey of the relationship between Blair and Dan. I think the reason Blair and Serena don’t work is because they will never fully trust each other and this all started from when Serena slept with Nate