You are right that Zoey asked the MC to come with her.
But Zoey left the MC because she left. She left. The thing we should be asking is how Zoey could leave so easily?
The MC hasn't graduated high school yet. What about Zoey? Did she drop out of high school or is she already done with high school? If she was already done with high school, it is selfish of Zoey to even ask the MC to go to San Diego with her and she is probably older than the MC then. The MC decides to stay, not only because his father would be alone, but also so that he can finish high school. In my opinion a reasonable decision of the MC.
Now what Josy once said to the MC applies. A relationship where you can't see each other every week sucks. That is in principle the reason why it came to the separation of Zoey and the MC. But in the process, Zoey probably made the first move because in the flashback of EP3, she presented the MC with a new boyfriend. The MC is free and then falls for Josy.
Is this perhaps what happened to Isabella and James? Isabella loses her job. She finds a new one at B&R and leaves. James can't come along so easily and Isabella goes anyway. It goes well for a while, but they both drift apart. James already visits Bella, but can't as often as he might like. Isabella and Jill have a sexual alcohol accident and just at this time James comes to visit Bella. He stands outside the window, as Jill does later, and sees his wife cheating on him. His reaction is to leave and not visit Isabella again because she has cheated on him.
The game within the game, or a repeated story, with alternating characters.