So the reason Phineas is the actual protagonist of the show is because there's actually considerably more focus on him than Ferb. Phineas is clearly the leader of their group and the idea guy, while Ferb is mainly just an engineer. A big part of this is the fact that Ferb doesn't talk much, which causes the focus to immediately shift towards Phineas and away from Ferb. There are also some minor details. Notice how whenever Candace angrily stomps up to them and demands to know what they're doing, she ends up mainly talking to Phineas, since he's usually the only one who responds. In fact, most people (aside from Phineas) don't even directly talk to Ferb unless he initiates the conversation. Also take note of how Phineas has three different catchphrases used in every episode, while Ferb is mostly silent, making Phineas a more dominant character. Overall, Phineas is the most important character in the A-plot, and Ferb mainly exists to give him someone to talk to (hence his silence).
I added Joe and Cleet and it seems like everytime I add the two as Arhtur's enemies you end up deleting something. In Dutch's eyes and mind he sees it as and believes that Arthur betrayed him even though that is not true. So from Dutch's view he thinks Arthur is no longer a ally or friend to him anymore but Dutch is wrong.
When I mentioned about Bill and Javier questioning Arthur and John's loyalty to Dutch later on. There are moments were Bill and Javier walk up to Abigail, Uncle, Charles and other surviving members of the gang questioning their loyalty. But those moments are so random you never know when they will pop up in the game. Bill and Javier even get mad at Abigail, Uncle, Charles and others when they think that they are betraying Dutch.
Actually Bill Williamson and Javier Escuella do become Arthur's enemies. When Bill and Javier side with Dutch and Micah they were ready to fight and shoot Arthur and John later in the stroy.
Later in the game there are also random moments around camp Bill and Javier walk up to Arhtur questioning his loyalty to Dutch. They also ask for Arthur to stop questioning Dutch's actions. There is a moment when Arthur and Charles are talking to each other and Bill wants to know what they are saying. Bill believes they Arthur and Charles are betraying Dutch so with all that evidence yes Bill and Javier started becoming enemies to Arthur Morgan. Infact before they side with Micah Bill and Javier start to get mad angry at Arthur during their conversations.
As for Joe and Cleet they are friends with Micah they joined the gang later on. When they joined close to the end of the story mode Joe and Cleet were not friends with Arthur they were strangers he didn't know.