I think you're correct that the father\son tension was a big issue for him. Particularly when he was a younger film maker. He doesn't come across as terribly deep in interviews, so his influences aren't too hard to see. Below is an article from a few years ago addressing the same issue.

That said; A much older and mellowed Lucas does seem to come at it from the other side in Kingdom Of The Crystal Skull and speak from the father's point of view. Indy is a somewhat supportive father to a rebellious child.

http://usatoday30.usatoday.com/life/movies/news/2008-05-20-lucas-father-issues_N.htm

Speaking of issues working their way into film; He's had another story arc that has shown up in two of his films that I've often wondered about, mainly because they both involve main characters. American Graffiti and Raiders Of The Lost Ark both have male\female relationships which border on inappropriate, age-wise.

Milner and Carol, after balking at having to spend time together, eventually start to enjoy each other and become close. Nothing inappropriate happens or is even hinted at, but it's very much an adult\child relationship.

Indy and Marion clearly had a past that was bordering on inappropriate. Marion mentions it directly; "I was a child. It was wrong and you knew it".

Because he was instrumental in bringing those four characters to the screen, I've often wondered if there was an issue being worked through.

For the record, Milner and Carol are my favorite part of the film. These aren't criticisms, just observations.