Whether or not one likes Shinji has always been quite divisive, but what is undeniable is that Shinji is the perfect protagonist for the message Hideaki Anno tries to carry across:
That communicating and connecting with others must be done, in spite of the pain it can bring about and the fear of rejection it instils in you.
I don't know what kind of disorders he would have, since I'm not qualified for diagnosing anyone, but what is evident is that Shinji's whole character is rooted in the fear of communication/rejection - this seems to be something that reflects a part of Hideaki Anno, since he mentions it in an interview somewhere. Actually, I'm pretty sure the majority of the cast suffer from this fear in their own way, but I'd be here all day if I discussed them.
IMO, Evangelion seems to be a very particular work, in that it is mostly directed towards those who have trouble communicating with others, or were straight up rejects of Japanese society (e.g. Otaku who lock themselves in their rooms) - that seemed to always be Anno's schlick, I mean for god's sake, he even worked on ME!ME!ME!, which was basically a message to otakus to get a life. Those who are already comfortable with connecting with others, or already have strong bonds of trust with others, may not find Evangelion as emotionally resonating.
But also, here's a video of Hideaki Anno participating in phone dates, which is pretty interesting and sheds some light on his views on his own work. You can even see a little bit of Shinji in him: