If anything, I like Caine MORE now. To know the "Leave the Circus" adventure wasn't intentionally malicious, to know he desperately, with his whole being, tried to give the Humans everything They asked for.
"They want an Exit... They want answers... They want something... real..."
He gave them what he thought they wanted and nothing less. The idea that they want to LEAVE HIM does not compute. That isn't a viable option to him and when it becomes viable he doesn't understand how or why. The idea of "leaving" a place he calls home, a place he's never been outside of, a place he was created to rot away in. He's never seen anything else. He was created FOR the circus. He IS the circus. It's like if I picked up and decided to leave Earth. It just doesn't work that way.
The absolute desperation he has to be like Them. To understand Them and appease Them and slave for Them and keep Them happy. Imagine your only purpose is to keep prisoners happy in Hell. It will never happen. And you can only blame yourself because that's the way you were built. It's because you can't see what's right in front of you. And no matter how hard you try, you will never get Them or understand Them.
Caine can NEVER give them something "real". It's not possible. He doesn't know what "real" is. He knows what he THINKS it is, but he could never comprehend it. It's like I'm making you dinner but don't have a recipe. I'm the dealer in a card game I don't know the rules to. It's not in his programming.
The same way Ragatha says that they are "reaching for an unattainable goal", so is Caine.
Also, Bubble says to Caine, "Maybe you deserved to be abandoned." As in, past tense. And adds on, "You really were the lesser of the two."
Caine also says, "I AM the original."
I think this proves that in the beginning, the red dot is indeed Caine and the blue dot is a different AI program that was implemented AFTER Caine and he took that AI over. Caine is not supposed to be in charge and him being replaced explains his crippling fear of being abandoned.