The Alvarez Arc was never about Zeref vs Natsu.
It was about Zeref vs Lucy.
And this may be a bit of a stretch but try to bare with me.
So the Alvarez Arc (AA) is essentially the arc of one brothers army vs another's. At least on the surface. But the main focus of the AA was Natsu's transformation and Zerefs reveal.
After Zeref reveals his and Natsus true identities to Natsu and Happy, Zeref then makes it a point from then on to try and get Natsu to change into his demon form, knowing that Natsu would probably have a hard time controlling it and would destroy everything and everyone in his path just to kill him.
Thankfully, Zeref was only half right. As evident by his four warnings to Gray to get out of his way, Natsu still had some form of control over his actions. This was because his only thoughts were getting rid of Zeref who started the war leading to Lucy's "death." He was driven by revenge, which was what Zeref wanted, as to why he painted himself as the bad guy.
But one thing Zeref hadn't really counted on was Natsus bond with one of his guildmates in particular. Zeref knew who Lucy was from the jump as she and Anna look basically identical. That and Anna and Zeref agreed it would be up to Anna's bloodline to look after the original eclipse project as well as the dragon slayers once they passed through to the other side. So right away, Zeref knows Lucy's goal is protecting Natsu and staying by his side.
So during the AA, it only makes sense that at every turn when Zeref thought he was winning, Natsu would make some miraculous return and start the fight over. But did Zeref know why or how?
Of course he did. Because that was the Heartfilia family's job. To protect and look after the dragon slayers, Natsu included.
So, when Zeref almost got his way the first time and Natsu "lost control," who brought him back to reality (with a little help from Erza)?
When Natsu was knocking on deaths door on the ground with a hole in his gut, who literally took on a curse that Zeref placed on the book, essentially risking their life to rewrite Natsus book, bringing him back from the brink of death to fi is the fight?
Even during Dragon Cry, Lucy is still a thorn in Zerefs side by showing Natsu throughout the movie that she'd always accept him no matter what form he took on, giving Natsu a sense of security, making Zerefs plan to break Natsu down until he's a mindless monster essentially impossible.
Every time during the AA and Dragon Cry movie when it seemed Zeref was finally going to get what he wanted, Lucy came in and snuffed all of his plans out like a candle.
And Zeref by the end could only watch as a human tamed one of his demons. His most powerful demon at that.
Lucy was even almost kind of acknowledged as Natsus reason to live. (As he did try to kill Zeref fully conscious of what he was doing and knowing it would kill him too when he thought she was dead.)
Zeref even tried to play mind games with Natsu but got blocked because the only thing on Natsus mind was Lucy and her life.
The entire AA is literally just Zeref telling Natsu one thing to make him feel terrible and Lucy reassuring him that it wasn't true.
Zeref even tried to make Natsu feel guilty about Lucy rewriting his book, essentially signing her own death warrent, only for Natsu to brush it off because he had more faith in her than some curse Zeref put on a book.
Every time Zeref tried to get into Natsus head, whether Lucy was there or not, her voice always seemed to ring through louder than Zerefs.
The entire arc is a battle for Natsus mentality and its not even being fought by Natsu.
Natsus fighting the physical battle, but Lucy was fighting for Natsus humanity. She was fighting for Natsus life.
In the end she won, and Zeref took the loss with a smile on his face, knowing that somehow a human girl had defeated him in a mental battle over his brother's life.
And he even took pride in it.
Pride in the fact Natsu had found someone who would go to such great lengths, even so far as challenging Zerefs curse power in order to save Natsus life.
That's what the whole arc was, a battle for Natsus fate. A battle that Lucy won and Zeref was happy about it.
Even Mavis knew only Lucy could challenge Zerefs power and change Natsus fate, leaving Lucy with the book as she went to help Natsu confront Zeref.
The one who decided Natsus fate vs the one who changed it.