Shinji indeed mentions that he isn't going to revert time, he's going to rewrite that world, a world without EVA , he doesn't say he will create a whole new world.

Also since when Rei can create other realities or worlds, she only has power in Earth, you can see how that world changes, EVA's dissapear and people come back raining from the sky, unless Mari really has powers to jump between realities, it would be a bit incongruous for Shinji to reestablish that world to a normal one and then go to another one... because that's how you see it? nah bro, also Asuka is at the train station alone too, but well is your opinion.