Is it a Bad Idea for Shinji to Stay With Misato?

You know how I define the whole Evangelion series? An animated pessimism! It seems that the real story never starts as soon as the optimism drains. What began as a usual mecha anime piloted by young kids, in what looked like a romanticized high school settings eventually went downhill. As the series ended, things became more depressed, darker and crazier, that it already looked like a different anime. But being crazy and sick is what brought out the charm of the Evangelion series, or at least as what the fandom claimed.