He as doubts and makes mistakes from time to time too.

And he has disobeyed his father on a few occasions. They were just things he Sisko couln't fault him for like teaching Nog to read or saving O'brien when Dukat's security program kicked in. Then there was the matter of the Dabo girl. Pops couldn't be mad at that.

As far as Obrien getting a lot of shine in season 2, it was on some other site I read that they made that move because he was thought to be the most relate-able to viewers. "Obrien MUST SUFFER" was the running gag of the writers for episode where they wanted to suck viewers in emotionally and Obirien being put through the ringer was the method.

I don't mind so much because the character is refreshingly blunt and easy to annoy for a Federation member. Especially where Bashir is concerned.