[Rahan]

Rin is not a double agent, she was under Madara's genjutsu.

Obito knows he was chosen for his abilites (hence not finding Madara's randomly), knows the Mist did something to Rin's body (and he should know she has no special abilities) and we know he later figured out the relationship between Yagura's master and Kisame (and Yagura was already controlled when Zazbuza was a child, hence before what's happening now)

Well, the timeline is now fixed. (as long as Rin is being brainwashed by the same guy than Yagura) But now, all that Mist's plotline with Kisame and Yagura's manipulation was just for the sake of brainwashing Obito, who is not thrash anymore, but the most talented Uchiha of his generation (since specifically handpicken by Madara) who is also able to harness Shodai Hokage's power intuitively. That's just errr ... boring ? wasting a perfectly valid plotline for nothing ?

As for Kakashi and his MS, it's the degree zero of storytelling. (lol he had it from the beginning)

At least, we know Obito's motivations now. He knows something was up, but he refuses to acknowledge them, so he 'll willingly collaborate with the one who set them in motion rather than the ones who were screwed by them. Because it's easier than facing the facts.
Good news is that it's almost over. Kakashi will say his sharingan saw the genjutsu. Madara will lol, Obito will attack him and he'll die, the story will move on, and Rin won't get a single line. There is only two chapters left to complete the volume and this sub arc.