It's interesting, because I often hear a lot of the same complaints about Stiles that I hear from some about Sam - that the whole show is about him and that the showrunner cares only about Stiles.
While he is part of the biggest ship of the show (which can dominate tumblr and the likes) and is portrayed by what I believe to be the strongest of the young cast, I can`t see the Sam comparism at all.
Scott is the one bitten and while in the world of Teen Wolf that doesn`t really make him that much special as there are other wolves, he is the one who is a "true Alpha" aka a naturally special snowflake who gets from a beta to an Alpha through his sheer goodness? It wasn`t that clear. And for the longest time he bemoaned his supernaturalness and wanted back to a normal life.
That to me speaks way more Sam than anyone else. Maybe Charlie in a Thompson-penned episode.
Stiles has only ever been the support, the comic relief and the sidekick. Okay, he got the brainy part of it but Lydia, one of the supporting female characters, is both supersmart AND supernatural (as it turns out). So he isn`t even unique there. Season 3.B is the first time Siles has gotten a story arc of his own. Which, granted, is a big reason why I believe the show rocks so much.
Now on account of Scott being the physically stronger as a werewolf and Stiles being a skinny, non-fighting dude, he wasn`t Dean-like in terms of being a physical protector. And he isn`t the only emotional nurturer because Scott`s mom fills that role to some degree. Maybe even Allison the former love interest. But he was, if you will, the "intellectual protector" of Scott early on. Stiles was the one researching werewolf lore and helping Scott deal with it day in, day out.
I`m not quite sure there is a Supernatural character that comes to mind readily as a clear-cut parallel but Sam? No way for me. I see basically no comparism.