so i’ve already been over the theory for Ruby’s “memory loss” is that he has PTSD (see: here)
but another theory I have is just that Ruby believes he’s too toxic for Sapphire
Let’s recap. Ruby is well aware that he has emotionally hurt Sapphire in the past. Back during the Salamence incident, while he was the one that got the physical scars, it’s the emotional scars he left on Sapphire that made him change his whole outlook on life. He’s also aware that he hurt her when he refused to join in in the battle against Hoenn after he saved her from the Grumpig.
Ruby truly does love Sapphire. He’d do anything to protect her, as most evident when he locked her in the air car because he didn’t want to risk the orb taking over her. But, as much as he does love her, he’s afraid of risking anything because he doesn’t want her to get too close to him, only to end up hurting her again. While he is fully aware that she loves him back, her safety is more important to him than that. (Also, since their confession was in the middle of a crisis, he did get some time to think things over before he met up with her again at her base to complete the 80 day challenge.)