The producers have actually said that "something" has taken over Sayid's body. It is most likely Jacob, and he could operate differently than the "Man in Black" AKA Smokey.
About the Parallel story lines: I actually think they are going to crash into each other at some point. They aren't exactly parallel, as one takes place in 04 and one in 07. I think, and its just a theory (one in which I can't exactly take credit for) that the 04 timeline where the plane doesn't crash is all a flashback. They are eventually going to all end up on the second plane, the Ajira flight that crashed, and somehow the Island will have been lifted from the sea and they all end up back there with their memories erased, except for Juliet's who somehow knows "It worked" which is why they brought her back again. This is what we are experiencing with the current 07 timeline. She couldn't have come back just to have another sentimental moment. That had to be an important element. Of course, this is just a theory, and I can't wait to see how it plays out. Hell, they may just run the entire season as two parallel universes, but I don't think its that simple.
Here's how the guy I got it from put it:
There are NOT two realities. There is the changed past of Sept 22, 2004 and the present (or 3-4 years later). The changing of the past does not mean a completely different future. The Island wants these people there and will find a way to make it happen. Just like Desmond saving Charlie again and again until he finally died. (in fact he says to Jack, "I was supposed to die")
We've seen the myriad connections these characters had before the crash (Sawyer and Jack's father. Locke's Father and Sawyer. Kate's Dad and Sayid. Claire and Jack.) and we've seen new connections made (Kate and Claire, Locke and Jack, Sawyer and Kate, Sawyer and Hugo) and over the rest of the season we'll see how these connections bring the characters together until eventually they end up on the Ajira flight that crash lands on the island 3 years later. (The stewardess with bad hair mentions that they were all on the FIRST flight)
I agree that we can't really establish a fight between good and evil between Smokey and Jacob, because really, I could never see them as either being inherently good or inherently evil. They have both shown elements of both.
I really can't wait to find out more about Richard (aka eye liner boy) and exactly what he is and why he doesn't age. If this isn't explained I'm going to be more than a little pissed.
Yeah, well, you know, that's just, like, your opinion, man. - The Dude