I have always been rather confused by Gendo's paper of choice. If he is only going to write "Come - Gendo Ikari", why not just write it on a normal, blank piece of paper? (Now that I try to picture that, it doesn't come off as aesthetically attractive + mysterious + foreshadow the father-son relationship tangle, ha.) Instead, Gendo chose to write it on some sort of an information page about Shinji - but with any possibly useful info obscured by a black marker. Does this mean Gendo originally wanted Shinji to read up on something but then decided against it? But it seems too intentional + too much of an effort to black out everything opposed to just get a new sheet of paper. I hope he didn't do it just for the sake of messing with Shinji's feelings.
Another train of thought, maybe I was led into believing Gendo blacked out the words by the "Gendo and Shinji (Relationship)" wiki page which says the following about the letter:
All of the printed words on the letter have been erased with black highlighter, replaced with a handwritten message in the same from Gendo which reads "COME -- Gendo Ikari". Moreover, Shinji has scribbled over Gendo's words in red pen and torn up the paper out of frustration at his father, later taping the pieces back together.
How do we know Gendo blacked out the words but the scribble and tearing were done by Shinji? I don't think there's any evidence to that (except educated guess based on their mental states... But wouldn't it also work if Shinji was the one who blacked out the words?).
TLDR: It seems a pretty weird letter to me and it's been bugging me forever. Thanks for reading!