Well, maybe you're right and it is some kind of transference, although Sam's character gets enough hate for that storyline himself. It probably didn't help that Amelia's first appearance made her look really incompetent, some people seem unable to move past that first impression.

I agree with you about the flashbacks. It's kinda ridiculous: First they reunite the brothers right away, but then they a) either put the focus on other characters (Bitten, Tiger Mommy, Blood Brother) and b) have an insane amount of flashbacks and thus break up the narrative. So what was the point of reuniting the brothers in the first place if they are not willing to actually spend any time on them and their current relationship? It feels like a stalling tactic. They had better told Sam and Dean's time apart in 'real time', thus not only their reunion would have felt more earned, but it also would have made for a much more coherent narrative.