I would say that the thing I've found irritating in early seasons was Nate's drinking. There are many occasions where his drunken recklessness has really endangered the team. The rest of the team members-Eliot, Sophie, Parker, and Hardison-are competent enough to pick up his slack. But in a dangerous job like this, it really rubbed me the wrong way that he would endanger them like that.
I know that alcoholism is a chronic problem and its very difficult to overcome. For years alcohol was Nate's only mechanism that he utilized to deal with the death of his son. At the same time, with moments like The Snow Job where he gambles way too big, not just with the money they are trying to regain for their client, but with his teammate's lives, I have to question where Nate's priorities were when he was in that inebriated state.
He comes back to redeem himself, certainly, but in the meantime, I wasn't too impressed with his drunk demeanor in many episodes.