I think Obito killed Rin.

Appearances:

Kakashi is wearing the same exact clothes he wore in the Gaiden & he still has the slit in his mask from when his eye got cut.



Look at the arm on Obito's Zetsu suit:



Notice the marks on this arm:




The Genjutsu

The blocky images that were shown when he saw Rin, are usually used when someone breaks out of a genjutsu with Sharingan.

Something similar happened when Sasuke broke out of Tsukuyomi.


I think Obito is in a genjutsu & he killed Rin in the Zetsu suit.

This:



is him temperately breaking out of a genjutsu, then Zetsu pulls him back in & shows him Kakashi killing Rin.

I think Madara used his Sharingan to cast a genjutsu on Obito & later Obito will use this eyes ability to control the Mizukage.

His eyesight:

Close your right eye and thrust your right arm out, compare your arm to the one shown in that picture



It looks like he's seeing from his right eye instead of left eye which Kakashi has open. Obito was seeing through his right eye, not linked vision with a Zetsu clone or his left eye that he gave Kakashi.


A long time has passed since the battle on the bridge.


Kakashi couldn't have been in the same exact clothes since some time has passed since the battle at the bridge.

Obito stated that some time has passed before his hair grew out:


It would take about two years for his hair to grow to this length: