On the other hand, Dan and Blair together represent the first true threat to Chair as the endgame of this show. My experience is that Chair fans are unwilling to recognize the evidence of a growing Dair relationship over the past season-plus largely due to this threat.
I don't think Dan and Blair is a threat to Chair as endgame. At all. I fully expect a finale reunion. I am a Chair fan and I can only speak for myself when I say that Blair or Chuck not together and facing a third party is not my issue with the show. I disagree with your characterization of the post 4x17 kiss and how it effected Blair. From a ratings perspective I think the Dan/Blair friendship worked better because it was sort of a backburner to better stories. When Dan and Blair went front and center as an actual romance it seems to have failed to connect with people.
I agree that they will go forward and tell the story they want to tell and I feel like the finale will make it clear what that is. One thing that I think gets forgotten is that Chuck/Blair has been the single longest and most consistent Gossip Girl story. It would not be fandom pandering to go back to them it would IMO be logical storytelling. I often feel like what we are watching now is Dan Humphrey Fan Fiction. In all actuality I think its just that the writers wanted to move Dan more front and center and that had to mean that he became involved in the CB Story so they made some big changes to the show to make that happen.
I also think this argument is very subjective. What you say is great storytelling I may think is crap. Someone can say that you need Blair/Serena fighting because that is the relationship while I think its the intense love they have for each other. None of us are right or wrong because it is just our opinions. Gossip Girl is never going to win an Emmy. We all have our belief over what needs to be done to fix the show or if the show needs fixing.
From a ratings perspective I think right now they just have to get over a million viewers. Clearly they need to try to bring people back. Perhaps in season 6 we will see some milestone episodes to try to entice past viewers to return. Right now Gossip Girl is not a ratings darling or a critical darling. It basically just exists. Getting a half a season is already embarrassing for a show that was once the best on the network.