Teen Wolf (TV series)/WMG

Derek's sister was an Alpha.
When we see her body, it's much more lupine than human, much like the Alpha and not like the little Bumpy-Head-Betas. In addition, Derek says "He's an alpha now " suggesting that the Alpha has only recently become so. This leads to the conclusion that to become an Alpha you have to kill the previous Alpha.
 * partially proven in a webisode. Derek's sister was an alpha, but how she became one wasn't made clear.

The Alpha is female
So far Derek and everyone else is only assuming that the alpha is male. In animal wolf packs, they are typically constructed of an Alpha male and Alpha female and their offspring. Unlike dogs they do not mate with their direct relatives and if one of the pair dies, then they either stop eating and die, the pack breaks up or they seek out a non related mate to bring in to help lead the pack. Maybe Derek's sister was killed so the unknown female could raise to Alpha status and perhaps is related to Derek  So seeking out fresh blood for the pack, the alpha attacked Scott.

The Alpha is the Chemistry teacher
He told Mrs. Mc Call that Scott needed a male authority figure in his life, which would make for a convenient excuse for him to volunteer for the job and spend more time with Scott (while actually training him as a werewolf). After the attack at the video store, the teacher was also very sympathetic to Jackson, telling him he could miss class if he wanted. His plan is probably to make Jackson another member of his pack (hence
 * Either way, the Alpha could have killed Jackson  and didn't.
 * Either way, the Alpha could have killed Jackson  and didn't.

Jackson is Scott's half brother
Combining two things mentioned that will probably become important (who Scott's father is/why he left etc with the fact that Jackson is adopted and the effect that's had on him). It would add to Jackson believing he needs to compete with Scott. Scott's father had a baby (jackson) with another woman and left. This theory is nowhere near full proof but could end up appearing as a red herring.

Jackson is a Hale.
He has been having nightmares about fires-- which killed most of the Hale family-- and is adopted. Uncle Burn Victim did twitch a finger at the inquiry that there was someone who had escaped the fire. With Jackson behaving so weirdly after being scratched by wolfsbane-poisoned Derek, (namely "Do you want a bite?" reaction, and reeling dynamically at the Alpha's howl,) it might be possible.
 * Jackson recently revealed that he's had dreams about a house and a fire. He also bears more than a passing resemblance to

Stiles is a Hale.
On his mother's side. Her death was arranged by hunters to look like an accident/suicide/disease since she was married to a cop who would otherwise track down said hunters if it was an obvious murder. However, she was most likely a cousin or more distant relative and only an Omega/low-rank, which is why hybrid Stiles has not wolfed out himself. The fact that Stiles seems to have a strange first name might reflect his mother wanting a traditional werewolf name.

Lydia is an Omega.
We already know that Omega werewolves exist, and are apparently the lowest form of werewolf. It's possible that being so low means they are unable to heal as fast as Betas can, if they even have accelerated healing.

Stiles's mother was killed by a werewolf
Stiles mentioned having panic attacks as a result of his mother's death, implying it was pretty traumatising to him. It's possible that the attack was dismissed as an animal attack the way the Alpha's killings were to begin with. Maybe it was a Hale, maybe it was another group of werewolves. Later episodes could have Stile's discovering this fact and it driving him away from the werewolves he associates with, especially if it WAS a Hale.

The Mountain Lion at the end of "The Tell" was sent by an Alpha
In "The Tell", when the school parent teacher conference seems to be under attack by the alpha. And it turns out after Mr. Argent shoots it, it was a mountain lion. I'm just thinking could the whole Brick Joke be a bit of Fridge Brilliance.

As all the werewolf incidents are dismissed as mountain lion attacks, plenty of people would continually find this suspicious. I believe the Alpha under this assumption somehow found a mountain lion and made it attack the conference in order to convince people it was simply all mountain lions doing it all and silencing all who found this suspicious.