Neal said he wanted her all that time but didn’t show her that
When did Neal say he wanted her? To her? After Manhattan I mean. And when he told her he regretted it every day, the next couple of scenes were them in the warehouse, Tamara knocking out Emma, him getting shot, the portal opening, him saving her from falling, and him falling through himself. So after he actually said he regretted leaving her every day, there was no time for action.
Neal’s decisions about Tamara and Emma aren’t so black and white like it was with David and Kathryn and Mary Margaret. David knew Mary Margaret wanted to be with him but he chose to stay with Kathryn instead. Neal had no idea if Emma wants to be with him. At that point, he didn’t know if she’d forgiven him. They were so far away from the “I want to be with you so I’m going to prove it to you” stage.
Neal was in the “oh my god I’m still in love with my ex from 10 years ago who I think still hates me but I have a fiance and I don’t know what I’m doing” stage.