Excellent addition from @just-a-river here!
And... I do wonder why the guy who hated change and deeply wanted his friends would change their names. And I think about the pointed mentions of him constantly rubbing his temple, struggling to remember things, and getting some things (like Pyrrha's lab number) confidently wrong, and how Harrow rewired her brain to autocorrect to "Ortus", how those names are censored both in Alecto's dream and to Nona in the present the one time Pyrrha names G—, how John and Alecto are so synced that they even share hunger pains, and all the parallels between John and Harrow, and... It's specifically always his right temple, and the right frontal lobe is the one more responsible for memory recall. So I suspect there might be a bigger reason at play...
But regardless of why he did that part, the ways his preferences have changed over time and the implications of those are always fascinating.
Going from the neoclassical lean to giving his daughter back her own name but Slightly different, now with a tie to her—his—their roots, roots he'd all but abandoned for so long, certainly says Something.
He named Her First, One. He's always known She was not a person, that She was something so much greater, despite the shape he'd made Her fill.
He named Her Alecto. There's still breath in his body. They're still out there. And isn't death what bad people deserve? (What he deserves?) Of course she'll help. She IS his vengeance, HE is vengeance and they are one. But then... Varun says "their vengeance is not my vengeance", and it's not 100% clear whose against whom, and Varun is clearly pissed chasing down John, but it begs the question... as filled with anger as She is, does She actually even want any form of vengeance, or do all those feelings come from John?
(We also don't actually know if an RB has ever killed a Lyctor (unless you count John himself and maybe Harrow lol); Cyrus and Ulysses and Cassy all died by their own plans to fight them, not the Beasts directly. With G1deon, we haven't answered the question of why Varun just left, or what happened to the cav crew that went to help... He does seem to be dead or somehow gone, but Pyrrha doesn't blame Varun, says he was always looking for something to throw himself on... For all their anger, are any RBs truly driven by vengeance?)
He named Her Annie Laurie. Just a woman. Just a pretty girl. Beloved perhaps, but mostly for those looks. The height of asking her to play pretend; absolutely nothing of her true self, a pure fucking insult.
He named Her Annabel Lee, and that's... not much better. It still makes Her so small, it's still so insidious in so many ways, still a gross warping of the narrative, but it also starts bringing some truth back into it, way more than Annie Laurie, and maybe about as much as Alecto.
Alecto the Fury is unceasing anger, and She has every right. But we've met Nona. We know who She can be and would rather be, if She has to be a somebody at all.
Annabel Lee frames him as tragic and mourning, which is true, but completely disregards his own culpability. The "angels in heaven" (his Saints) and "demons down under the sea" (the ten billion who haunt Her original corpse and are almost certainly part of the reason he can never return) certainly did play a prominent role, and She acknowledges that too—he did it in part to appease them—but they aren't the ones who put Her in the Tomb. It frames Her as precious and innocent, which She is, in the same way nature is, because She is nature, and just as powerful and terrifying. Her power is both Life and Death. And the framing as Annabel Lee doesn't do that justice at all.
"No other thought than to love and be loved by me" is a bit of a double edged sword, too. "In the year of nobody she thought about that much in particular" is such a funny fucking contrast to it. And at the same time... it's not Her name(s) that unravels Nona. Kiriona say "Alecto, Annabel, I don't care whatever her name is" a good minute before, and despite Her fear earlier when Pyrrha almost says it, nothing happens. What unravels Her is "John loves Alecto. John needs Alecto." And then She devolves, into he loved her, she loved him, for he had loved, for she had loved, for the world had loved, love, love, love...
And of course... None of them, not the Saints, not the devils, probably neither her kin nor his, "can ever dissever my soul from the soul of the beautiful Annabel Lee."
And no matter what the motivation for any of them, none of those are Her name. We call Her—Them—It—Alecto. The last book title names It Alecto. But that is also not Its true name. It has many names, and has as long as there's been language. It's Earth. It's Gaia and Terra and Geb and Hòutǔ and Bhumi and Ki. It's Papatūānuku.
And... It's also not, anymore, I suppose. Because they are the God who became man and the man who became God. Part of the horror of John's existence is that no matter how badly he wants to still be human, he can never truly be that again, and part of Alecto's is no matter how much It hates being at all human, on some level She now forever is. Their souls have bled together and there's no going back.
A little tangentially, some of the other things John references might also have some implications about how his wants have changed.
"How sharper than the serpent's tooth" from King Lear, famously forgiven by the daughter he'd disowned and treated terribly. Also I mean, both die at the end, but considering...
"Why have we not an immortal soul? I would give gladly all the hundreds of years that I have to live, to be a human being only for one day." From The Little Mermaid, the original one. The one where rather than remain human, the mermaid melts into seafoam. It's a tragic death for the mermaid, and would be a death for John, but for Her... wouldn't that just be the best possible outcome? To allow It to return to being the sea...