Hard to say since most of them are intentional because of story or they don't follow until end of manga and may fail to properly explain.
Serial Experiments Lain, Boogiepop Phantom, Shiki, RahXephon ...
and of course Tsubasa Reservoir Chronicles when later in manga goes even more confusing
Evangelion 3.33
Didnt know what was going on most of the time...
rewatched it and then it was bit clearer
well, pretty sure the director wanted it that way and make the grand finale in the 4th movie
hopefully they answer all the questions in the 4th one
I liked the episodes 1-21. But I was like 'WTF?!' When I saw the ending. Really? "Omedetou"? And the Movie The End of Evangelion: You are (Not) Alone made me confuse as well
Neon Genesis Evangelion, it's not just confusing, it is also bs.
A real shame, I liked the animation and how they set the characters... then the series had budget issues if I remember correctly that just resulted in a hack-job.
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