The entire Village scene is mainly about Shinji's recovering. In an actually healthy and welcoming setting, contrasting that of 3.0, surrounded by people who care for him, Shinji is urges and eventually agrees to socialize, go out into the world, try new things, help and feel part of the society by fishing, etc. He gets to feel human again, finds a reason to fight as in these people and this oasis of humanity, and it could even be argued that the contrast between Shinji and his once classmates, who are now respected adults with families while he's still a crying kid, was a wake up call too.
All of this culminated to Shinji's response to Rei's death and him finally escaping the vicious cycle of good times followed by horrible tragedies and then his downfall due to him being unable to accept them and move forward. This time, he merely takes the first step, exactly because of what happened prior at the Village. He isn't magically healed, as despite the two flawed instances in the rest of the movie where Shinji displays an unrealistically stoic, unresponsive behavior to tragic events, Shinji very much does not have all the answers and still grows throughout the rest of the movie. That's why he contemplates, hesitates, and continues to make important realizations like when he finally accepted Kaworu's death on the Wunder.
decides to use the godly powers of his EVA once again (just like his "immature self" tried to do in HA and Q, but failed) and then creates a "perfect" world in his image. He, for example, "fixes" Asuka without asking her what she wants and sends her away without even giving her a chance to say anything. Then he proceeds to destroy the power he used to do all of that and labels it as the source of all people's problems. That's, at least, hypocrite.
OG Shinji: "I'm giving people the possibility to get out of Instrumentality, with the free will that's inherent to everyone. The real world isn't perfect, but I rather live in it than in a lie."
NTE Shinji: "I'm using this godly power to create my vision of a perfect world, because I know better than everyone. Then I'm destroying this power because it's bad."
Not really though... Almost two years have passed since this movie's release and, for me at least, the only interpretation of the ending that makes sense and agrees with the many important details and clues in these last few scenes is that Shinji doesn't literally create a new world, nor does he reset the world or turn back time (as he says so himself). He merely wishes that all Evas stopped existing from that point onwards. No one loses their memories, no one else should even logically have come back to life outside of Asuka (not even the people inside the FoI), and the red contamination around the Earth only disappears because it's caused by the presence of Angels / Evas (recall Neo NERV's flying ships, how Bethany Base in 2.0 where Angels were being experimented on was guarded by Pillars, how Asuka in 2.0 after being infected by the 9th started emitting this same exact contamination and had to be contained with the Pillars), and so when all Evas, including the FoI (with their also distinctively red color) scattered around the world disappeared, so did the contamination. Ultimately, only Shinji and Mari who promised to everyone to come for Shinji (and is probably also paying the debt to her best friend Yui by doing so) remain stranded inside the Anti Universe with no Eva to get them out. Because the Anti Universe connects fiction (the Eva universe), with reality (hence why the Giant Rei that came out of the Doors of Guf was so realistic - looking), that's where these two eventually end up, in our world, where the figures of Rei, Asuka, and Kawuru that Shinji sees across the train station are merely visions and are closely framed as such.
What I want to emphasize though, is that to make his wish in 3.0+1.0 Shinji agrees to sacrifice his own life, an instrumental detail that changes the context dramatically and is too often forgotten by some. It's this detail that renders criticisms of the ending being an escapist one as frankly nonsensical.
So, in EoE, Shinji's decision, not what ultimately came out of it, was that everyone should die basically because no one understands him. In 3.0+10, he decides to give his own life so everyone else can life in a world without Evas. The Evas aren't the scapegoat, it's always been people that are at fault hence why the final confrontation is between Shinji and Gendo and not Shinji and some unnamed Eva. They are merely a symbol, arguably of the means that allow people to realize their escapist, destructive wishes, and certainly of the Eva franchise itself. After all, there's a reason why in promotional material for the film, in the slogan "Goodbye, all..." the word "Evangelion" and its plural, "Evangelions", are used interchangeably. This last symbolic level of the Evas is most probably why this part of the ending even made it in tbh. The plot is already finished by the time Shinji makes his wish, and it would only had been easier and perhaps even better "fanservice" if the movie just ended with Shinji cancelling the Impact and returning to Earth to rebuild the world with Asuka and any other survivor. Hell, they even have the Pillars and the means to transport them so they could even slowly work to clean up the entire Earth.
Nor is Shinji's wish hypocritical, because to destroy the Evas he must also destroy himself. I am emphasizing this because this is Shinji's mindset throughout the ending. He doesn't discard his friends, he's merely saying his last goodbye to them because he's going to die. He isn't resulting to escapism again, because he won't even be around to experience the fruits of his supposedly escapist wishes. He never expected Gendo and Yui to take his place, and so everything that happens after this point is unplanned and out of his control. The fact that Mari joins him is out of his control and the different world he ends up in is out of his control. As for Asuka, I do certainly have my doubts about how effectively her conflict with Shinji was involved, but I have to say that Shinji simply used the properties of the Anti Universe and of Additional Impact which he was the center of to pretty altruistically help her. Yes, I do think the second scene of Asuka's sequence has no time to breathe, but arguably because of the ambiguity around Asuka's feelings for him in the end, Shinji wanted to send her somewhere he knew from first hand experience she would be safe (close to Kensuke, asn individual who she just realized has been the parental figure she has always longed for in the previous scene), before she made any stupid decision like deciding to stay right there with him.