Ok. Just watched this anime and the ending, like everyone else had me confused and bothered. Seems vague but after reading several discussions on forums I think I can break it down and explain the reality I haven't seen anyone else come to:
To understand what happened you have to think like the writer, and what thematic point they're making. Thesis is the main message of the story, anti-thesis is the narrative tool to highlight thesis, using Protagonist and Antagonists to represent these ideas. Shu and Inori are thesis and Gui and Mona are anti-thesis.
Shu's battle is against the selfish, survival of the fittest "natural selection" of human nature represented by Gui and Mona--who only seek to reproduce themselves, also Doth who represents the natural drive of reproduction. Shu's selfless nature and Inoris innocence represent the opposition to this.
In the end Gui wanted to save Mona, Shu's sister, because he couldn't care less about anyone else and was willing to sacrifice all of humanity to be with her. Remember when Mona talked to Shu about Triton looking at her? Triton liked her and still did to the end. In the end Gui went to Mona's traumatized body before the lost Christmas event to be with her to save Shu's sister but they both died. However, since Shu was absorbing all the voids he took Gui's void power, his king power. Eve represents the potential to create a new world. Shu could have created a new world but with Mona's body gone there was no person to house the EVE creation power, but Inori was the whole time created solely to house the EVE power. Inori was preserved genetically with her last tear that dropped and crystallized as the flower Shu took hold of. Having that Shu basically had Inori's soul.
This is where people miss the point, Shu had the king's power and could create the new humanity but EVE was gone. Inori was still existing though and came to Shu. Shu used his Gui void power to Bring EVE out of Inori, since that's the only way he could be with her---he took the seat as king and made Inori INTO EVE--remember Inori was a copy of Mona, and had the EVE power to remake the world within her--Shu just needed Gui's power to bring it out of her.
Since he was able to bring Inori's latent EVE power out Inori offers Shu her cradle, which is red string representing her soul and he took it, basically finalizing the creation process, HOWEVER, Shu did not destroy the world and remake it like the antithesis (Gui and Mona) were planning. INSTEAD he took Inori's soul like Gui wanted to do with Mona, to be one and with her forever, and he gave the world life by not destroying it and ridding it of the void plague.
Shu was still alive but at the end he and Inori were 'in heaven" (or the crystal plane as they said) together forever, their souls and hearts one, just like how Gui and Mona planned. As for Shu losing his sight--he rid void powers from the world, and his void power was connected with his eyes, since his eyes were what drew out the voids of others, so when he got rid of the powers his eyesight also went. I think it's coincidence that Inori couldn't see due to the crystal plague that had almost totally consumed her body.
So to conclude, Inori's body was gone, but she became EVE (a new "Eve") in the process and took over the role as the force that provide the power to re-create the world, and since Shu took the cradle, signifying his unity with her as king, they both lived in heaven together for eternity from then on. He didn't lose her at all, their souls were united (and she isn't just some distant memory. He's really with her there in the other world and she's very much alive). If Shu healed Inori he would've died having taken all the void plague and she would've lived without him, she chose to give him her power as Eve and offer as an alternative to be Eve and let them join in spirit, which let them be together and still (even though she's just a soul in 'heaven/crystal world') save the world from the void plague. The alternative was Shu saves himself but the void plague kills Inori. If either of them were selfish one would've lost the other. It's such a heartbreakingly warm story and hits you in the feels to know they transcended any level of love if they both lived physically. Their love truly rules all and would last forever.