Theory time!

My gut feeling tells me that Adam's eyes are his ex's/Isaiah's ones when he lost his vision (picture with hospital gown and eye sockets bleeding with bandages on Adam's leg during Eve's dream). Before the "incident" or romantic relationship between Adam and Michael, Isaiah and Adam's eyes are the exact same color; and after Eve rejoins civilization, Isaiah's eyes are one light grey and one black. So, perhaps when that incident happened, Isaiah did not want to lose Adam and sacrificed both of his eyes to make a successful operation to regain his vision; nonetheless, Gabriel, Isaiah's esper, also did not want the genius scientist who helped stabilize espers' conditions to lose his vision; so, he also offered his eyes.

Since all three, fortunately, were blood compatible to exchange their eyes without their bodies rejecting said new foreign organ/autoimmune reaction, Isaiah and Gabriel made a deal to share Adam's & Gabriel's eyes. That's why both of them have one light gray eye* & the other black. So, they may be a little blind from said gray eyes (which were Adam's damaged ones on vision), with some body modifications for battle enhancement on Gabriel's as he has a slight green color on his gray eye as he is the esper always prepared for battle.

Moreover, Michael was chocking Adam when something did not go his way immediately while both were having their first sexual encounter. So, maybe now, our Adam unconsciously likes "to feel a little pain" during sex as a consequence of Michael's sadism which he has been unaware of after Michael conditioned him for that and wiped his memories, but Adam's body still remembers...like muscle memory. Also! perhaps those red wave dots when Michael/Eve feels excited/thrilled towards Adam might be a subtle sign for his sadistic/posessive "switch on". Meanwhile, the white wave dots are Michael's imprinting on Adam (plus a funny coincidence note: Michael's request to only kiss with Adam was also punishment to not do it from Adam when Eve almost attacked Isaiah, so Eve immediately dropped the act and cried).

Plus, those "recordings while giving a testimony" from Adam gives an eerie feeling that humanity might have succumbed to carnage already where the gates opened for the horrors to annihilate everyone while Eve went berserk to protect humanity but he, perhaps, also could not distinguish from ally or foul and eliminated both for more despair to succumb to.