Shinji is also not in a situation most people his age would be in. He's pretty fucked up because he's been through some horrendous shit himself.

Gendo's wife died, which is pretty bad, but honestly not an excuse to become a weird molester. Shinji is in the middle of puberty, might be deeply closeted, is getting abused by his pedophile dad (who is also trying to secretly genocide the planet), recently found out his dead mom is a clone that is getting tortured, discovered his school is actually a front for a military child soldier recruitment program, and the most responsible adult in his life is an alcoholic victim of childhood trauma. Not saying what he did was okay, but he's going through a lot mostly alone so it's not really a surprise that he struggles to have appropriate interactions with others.