-Dean gets shot in the left shoulder (by Meg!Sam) around the beginning of February, 2007. (entry wound only)
-Around five or six months later, Sam gets shot in the left shoulder by Bella.
-Almost exactly one year later, Dean gets shot in the left shoulder again by demon!FBI around the beginning of February, 2008. (entry and exit wound)
So, Dean's left shoulder would have been pretty damn messed up until Castiel gets rid of all his scars in S4.
Season 4 rewatch
Ok, I've only watched three episodes, and one of those doesn't even have Sam in it....but MAN, I am suddenly REALLY noticing how controlling Dean is. I think I'd want to get away from him too. I think the first time I saw the episodes, I was too focused on the plot, and the second time I was too focused on Sam's behaviour...but, yeah, now that I'm watching again, I'm really starting to see what Sam was talking about. It makes me really interested to see what their relationship is going to be like in S6.
It also points out that Dean actually DID have a long way to go in treating Sam like an equal, not a kid.