I mean up until he accepted reality, things kinda were worse off. Rei killed herself (and then her replacement gets killed too), Asuka had her mind eaten and her baby taken away, Toji...okay, I'll admit, he's better off.
Even when all that disappears, it's still kinda bittersweet. He's with the real Asuka now, but he gave up the potential perfect life he could've had with her into order to live with her in hell on earth. Though I agree, it did end on a happy note, though how happy one can be in what's left of earth is beyond me.
Also, what was the point of showing that kid at the end of it? I doubt there will be a sequel to cover what happens next (though I wish there was)