I do think that it's easier to notice parallels when you read meta and see all the navel-gazing on tumblr, but the brother war parallels in seasons 4 and 5 became overpowering (and for me ultimately hindered the story, as character growth took a backseat to rehashing which brother had more pain and how many times they needed to be reminded they had nothing but each other). The nadir was Barry Bostwick as the magician yelling about how the guy he killed "WAS LIKE A BROTHER TO [HIM]!!!!"
I probably didn't notice because I was actually invested in the story for once (I wasn't a big fan of seasons 2&3 when they originally aired, either. Actually, I'd given up on the show, then one day after season 4 ended I decided to watch 4x01, loved it, then binge-watched the rest). I DO remember rolling my eyes about Sam's demon blood storyline, though. I used to hate Sam, and I was already bored by that point of the brothers' dynamic, so when Dean was all "If you walk out that door, don't ever come back!" I did not care at all, haha. The bigger things like the Apocalypse happening in the background helped me get through the tough times!