I know an adult anime that may very well have seriously influenced The Matrix (besides Ghost in the Shell)
Serial Experiments Lain
I've grown think of the world as a giant Photoshop Canvas. We are on a busy layer with some above and beneath, with relatively little in them. Most things on the other layer are too low opacity for most people to see, and most of the time our layer is locked... but every so often something is disturbed. I never used to think about other facets of 'reality', but as a god believer I think there is another realm but it need not be some crazy outlandish thing. Also as a therianthrope and having experienced things like phantom limbs, Its lead me to question my own perception. Well, I just thought of the phantom limbs like amputees with phantom limb syndrome, but the fact someone SAW them made me radically rethink things.