Warning: Spoilers for Supernatural, All seasons.
Problem #1
First and foremost the entire point of Season 6 is to get Sam's soul back. The main issue at the end of Season 5 was that Sam's soul was in the Cage and therefore untouchable. Now this was handled by saying people souls are small enough to slip through the metaphorical bars, which was done by Crowely.
Question #1:
Now that Sam's soul is in regular Hell and not Cage Hell, why the hell hasn't Cas popped down to rescue it? Seriously, it would take him 5 freaking minutes and he OWES Sam. Not only did he help the boys start the apocalypse but Sam went to Hell to save the entire freaking planet, Heaven included. There should be a little good will going his way. Crowely was the King of the Crossroads because he wasn't as powerful as Azazel, Lilith, or Alistair. Just because they're all dead doesn't mean he's suddenly more powerful. He just has less competition.
Question #2:
Demon Killing Knife. Where did it go? Why haven't they just stuck Crowely in a devil's trap and threatened to gank him to get Sam back?
Question #3:
How can Sam be wandering with no soul? All the Supernatural Lore indicates that something must be in the body for it to wander around. Sam is currently empty. He's a computer with no OS. He should not be running programs.
Question #4: Why did everyone BUT Sam get a happy ending? Cas came back from the dead. Bobby came back from the dead. Dean was finally in a position where hunting was something he could choose to do. How can the writers justify Sam getting the short end of the stick? (Again, I might add, because when have things ever gone right for that boy.)
Problem #2
Why is Sam always wrong? About everything, forever?
Case #1
The first person in the series to have nice feelings about a Demon was actually Dean, in Sin City of Season 3. There is this scene at the end where Sam shows up and ganks the demon and Dean is all trembly lip. The audience has a moment of "Oh noes!" and feels all awkward at Sam for killing the damn thing. Yet when Sam gets cuddly to Ruby it is immediately a Bad Thing and there is no redeeming feature of that relationship.
Case #2
Quitting Hunting. Let's face it, it's a crappy life that pays shitty. It's blood, death and chaos all the time and the chances of something going wrong quickly are very very high. Can you imagine having lived that during high school? Instead of dating you're off killing werewolves and ghosts. You move to towns specifically because people HAVE died. There is always a chance that you or your family is going to bite it over the next 24 hours. It's unarguably sucky.
But when Sam wants to quit he's a traitor to the cause and to the family. Wanting to have some independence and grow into himself as a person registers as a Cardinal Sin. He's seen as having abandoned everyone.
When Dean quits it's this giant celebration and everyone is happy that he's realized that hunting isn't all it's cracked up to be. Everyone is happy for him for having 'escaped' and proud that he hasn't fallen back onto the bandwagon.
Seriously, WTF?
Case #3
John. He is a bad parent. He may love his children but he was a crappy dad. He was neglectful, emotionally abusive and knowingly dragged his children into dangerous situations.
When Sam points out he was a bad father he's once again vilified. We as an audience are exposed to Dean's view on how their Dad was just trying to keep them safe and exposing them to the truth so they didn't get eaten in the night. But the moment Sam in on board with how John treated them Dean changes his tune and we here about what an awful Dad John was.
Notice a pattern? Furthermore, Dean's opinion is always given more weight by the writers. Sam, even before the whole anti Christ bit, was the character who was doing things wrong and being vilified. How can this show be about two brothers when the writers have a hate on for one of them? Now don't get me wrong, I like Dean, but I like Sam more. He's more realistic and more complicated. And for whatever reason the writers seem to use his real life issues as a way to make him an antagonist for Dean time and time again. This double standard is really starting to tick me off.
Yeah, Dean lost his Mom, then his Dad, then went to hell, came back and was supposed to be a Michael vessel. Struggled with alcoholism. Has currently lost his girlfriend. Dean witnessed directly the deaths of his mom and brother (x3)
Sam witnessed his mom's death, his dad's death, his brother's death (x101), his girlfriend's death, and had to shoot a potential girlfriend. He died, was pulled from Heaven, discovered that Angels HATE him because his mom sold the rights to his blood to demon (which caused Mom, Dad & gf to die), became an addict when the people around him KNEW how to help, was betrayed by his next serious girlfriend, was betrayed by his brother's angel friend, took all the blame for starting the apocalypse (1 seal of 66 that he was SET UP to break. And Dean broke 1 too!) WAS taken over by Lucifer, was thrown into the Cage with Lucifer and Michael, and is currently missing his soul. Oh, and freaky evil psychic powers given to him by demon. And he's still seen as being the 'bad guy.'
Short end of the stick, meet Sam Winchester.
I'll add more show problems as I think of them.