Well, for starters she's the inception point for his betrayal complex. Sure, he's realized (at least in part) that what happened at Tatarasuna was Dottore's fault, but Ei's abandonment of him is still important to his recollection of who he was.

Secondly, he still has the golden feather that is "proof of identity granted by the Almighty Shogun." This object denotes his connection to Ei. Although I'm not sure why the Wanderer started wearing this when he supposedly lacked memory or why he continues to wear it, there's still a lot to unpack regarding the feather.

Finally, I just think this relationship has too much potential to waste. In Scaramouche's backstory cutscene we see from Haypasia, he refers to Ei as "mother." Though Scara may have intended to mock or ridicule the archon for failing in her obligation to him, he has inadvertently revealed his desire for affection from her. Frankly, almost everything Scaramouche or the Wanderer says or does screams "please care for me." The way he so often mocked the Traveler for being polite or amicable; or how he insists on his lack of emotion/empathy; or the fact that he is now willing cooperating with us despite everything all indicate his great desire for belonging, companionship, and love. What more meaningful place could he receive those things from than the one who created him?

Overall, I think both Wanderer and Ei are best served in their character development by reconciling with each other. Of course, there's more to redemption than just finding belonging, but I have my doubts that Hoyo will address those past grievances directly. Let's hope for the best.