I don't think Evangelion was that controversial either. Definitely in depth and very hard to understand but not controversial.
As for Death Note, its true that it opened an interesting can of worms but it was still Fictional. I think it would be more controversial if Kira never had a "death note" and instead was a Japanese Dictator. That would be much more controversial I think cos it would be dealing with real world issues and the content could be taken much more directly and seriously.
Not everyone is good at looking "beneath the beneath" sadly, which is what a lot of Japanese stuff requires.
ps. I think Marmalade Boy for its time was quite controversial
