I think on paper both characters started out thin and cliché. That early draft by Kripke? Horrendous. Gladly someone reworked it but Sam was so clearly the pimped-out Sue and Dean so clearly nothing more than the dumb jerk who was held as a negative mirror for Sue!Sam. It`s also uncanny if you read some of the tie in scripts. Both characters are completely unlikeable and flat. You hate Sam for his Sueness and Dean for being a dumb jerk.
Where I think Jensen excelled was taking a character like that and bringing enough charme, fun and charisma to the role that it softened the edges. The writers also gave him more emotional exploration and layers and he ran with it.
However, I never doubted that Sam was the main character early on. He was at the center of the plot and had the destiny and the powers and the angst coming from it. Unfortunately they both overpimped that aspect of the character too much and Jared didn`t really play against it so the combination didn`t work for me.
Surprisingly, I found myself Sam liking more and more over the course of Season 1 and 2 regardless (whenever the Sue-plot didn`t rear its ugly head) because I felt his growing relationship with Dean, them learning to be brothers again was really heartfelt and touching. And my issue with the character having a certain sense of superiority was neither so bad that it tarnished my enjoyment nor had I lost hope they were going to address it. I mean, I expect characters to be more flawed early in the show, that`s what the show is for, to mature them. Dean had his fair share of flaws I wanted to see addressed, too.
Season 3 was iffy but it`s hard to truly judge it because of the writer`s strike curtailing it. I know the original plan was Sam Sue-saving Dean, though, and having once more everything in the history of ever be about him and I would have hated that.
Season 4, I felt Sam was at his worst in a way but I didn`t mind it. I didn`t find the character too unsympathetic while it happened. Sure, his superiority shtick grew five sizes but I was so confident that it would lead to the betterment of the character. And his motives weren`t unrelatable or anything. Then Season 5 happened and wow, talk about: hope. dashed. Dean gets the blame for Season 4 Sam and Sam gets the ultimate Sue-save. That broke the character IMO, not his dark arc.
Compared to Dean`s dark arc this Season, Dean`s flaw which led to the bad decisions was actually the one that always bugged me as much as Sam being smug. The family patheticness. You wanna talk about having no sympathy for a character? I had none, none whatsoever when Dean made the deal. Like foaming at the mouth mad at the character. This time around I was admittedly happy that he got the mytharc for a change, no matter what shape it took and I didn`t hate it like I hated the deal. We`ll see if at least this will be used for the betterment of the character.
In general, though, while there was always more emo-stuff for Dean then for Sam - and I have to say, in lieu of Sam hogging all the plot, what else would anyone have given Dean to justify his screentime? Nothing? I hated that stupid divide of only plot vs. only emo (and since I prefer plot, I hated that Dean was at least on the wrong end of it) but Sam couldn`t have all - I don`t agree that there wasn`t any POV of Sam. In fact, there have been episodes set entirely in his head. No other character, to my knowledge, has gotten that. The problem was just that these episodes didn`t help me make the characters more relatable. Quite the opposite in fact.
I mean, imagine you go "hm, I wonder what Sam is thinking?" and the answer is "oh, his version of his Mom tells him how cool he is and how much better than his dumb weak brother" or "oh, Death is fellating his wonderfulness". The hell? Without knowing what the character thought for sure, I betcha even the most unfavorable thoughts wouldn`t have made him out to be THAT dickish. What were these writers thinking?
I remember an old Star Trek TNG episode featuring a "what if" scenario for Picard on what his life could have been. Now the Picard we know is large and in charge, wise but tough in his own quiet way, a leader. The episode had him be a low-ranking timid Lt. who never went anywhere. That endeared viewers to a character. If the SPN writers had gotten their hands on it, it would have probably featured him as the High Admiral of the Federation who just negotiated a universe-wide peace treaty. With Sam, they seem kinda tone-deaf in their attempts to make the character more beloved.