>>283549541 (OP)
I think what makes Eva so successful, apart from having such strong characters and themes, is that its plot really isn't nonsensical. It's told in a way that is purposefully confusing and a handful of key details weren't revealed publicly until later on, but if you're willing to put the pieces together you'll find it's actually very internally consistent and basically everything in the story has an explanation and makes sense. At this point, the only things that are really ambiguous are certain character motivations and thematic intentions.
And yeah, again details of the plot are obfuscated to the audience sometimes, but the fact that they wrote the show with an internal lore bible means that everything is consistent and makes just enough sense to draw the audience into the mystery and reward them for paying attention and digging deeper. There never comes a point where you hit a wall in understanding and realize you're wasting your time; instead, you get those "oh, so THAT'S what happened" moments. (at least this applies to the original series, the Rebuilds are a different story and I think suffered a bit from not being so well thought out)
Something like FLCL I don't think the plot is that important because the show is clearly intended to push the boundaries of anime as an audio-visual medium, and not a narrative one. And I think you have to approach it with that in mind.