Why does Evangelion manga's plot diverge from the anime? I have read the manga, all of it, and I have watched the first 13 episodes of NGE. And it surprised me, because the plots were different with the manga (well, just some of it). Especially the ending in manga. I wonder why the ending and the plot were different? What's the reason for that?

And how was the manga made in 1994, while the anime aired in 1995? Which one came first? Was Evangelion based on manga?
Because the manga is by Yoshiyuki Sadamoto not Hideaki Anno. I think he talks about it somewhere. Sadamoto simply had a more positive view of the story, so you see Shiji talking more. Not even Anno himself sticks that much to the story as the fans do, see Rebuild series. So, relax and enjoy.