I didn't fully understand the ending until not long ago. I was just a bit hazy about certain things (Seele want to destroy the world for their plan, and Gendo also does, but somehow Gendo doing it is against what Seele wants, and then Shinji ends up being the one with the power to reshape reality, and he's the worst candidate in the world for that). But then it was explained to me.
Kinda' like the plot of FF7. I missed a few things here and there (the first time), remembered stuff in the wrong order, the game wasn't clear about a few things... then a website explained everything clearly.