Yellow Echo-Eye Does Not Mean ____ Is In Control!!
A lot of what backs people up on thinking that Rhys is being controlled by Jack in present day is that his Echo-Eye is yellow. But that doesn't mean Jack is in control. If you remember when Jack actually took over Rhys his eyes remained blue. 
at about the 25 minute mark you'll see that his eyes remain the same color. But also remember what Jack did to Rhys at the end of episode 2? He hacked into his subsystems. Going into the subsystems may have triggered this yellow color because Jack might know more about how to unlock the power within the Echo-Eye. So i think the yellow color is just showing that it's more powerful not that Jack is taking over.
Edit: also if you pick Jack at the end of episode 2, the drones he controls are colored blue while the ones Rhys controls are colored yellow.
So what do you guys think about this?
Comments
Although it could be possible that Jack hacked himself into the Hyperion database or that maybe Rhys and Jack have been combined to form one personality. Rhys does seem a bit more like a dick in present day, but not enough to say he's Handsome Jack.
I completely agree that Present Rhys is not being controlled, while I didn't let Jack in anyway, I think we would have known for sure or not if he was already. After seeing some LP's where Rhys and Sasha come back and Jack has some temporary control, his mannerisms are way too apparent to say he's in charge in the current. There's no way that Jack could hold back any of his enthusiasm and Rhys acts just like himself in the present.
Now I did speculate it in another thread but I'll say it again here. I think Present Rhys actually doesn't have Jack in his head any longer and that Jack has integrated into Helios. Jack has fairly limited control in Rhys, but imagine he got the chance to get into Helios' system, the king is back in his castle.
And his yellow echo-eye to me is nothing more than a upgrade he got. His robotic arm, clothes, haircut, and even Fiona's outfit are unique. So I assume maybe when they get back to Helios they treat themselves like queens and kings but obviously things go bad and they end up back on Pandora.
I agree! This does make sense and opens up a whole new possibility for Borderlands 3!