I get pretty obsessive about this, so forgive the long post!
The smoke monster. It's been harassing them since episode one and continued to harass them until the very last.
Not quite. The island has always had a caretaker, and both Jacob and his brother were potential candidates for the job. Then Jacob's brother (who is never actually named for some reason) kills their mother, who was the old caretaker, and Jacob in his rage cast his brother into the light at the center of the island, turning him into the abomination we know as the smoke monster by embodying the brother's anger at the world he lived in.
I was kind-of hoping for it to be an ancient demon or a bio-mechanical nanocloud or something like that, but I liked the island backstory as much as I would have liked either of those, so it was good for me.
The polar bears were kept in cages and experimented on by the Dharma initiative. When that fell apart, they broke lose and managed to survive despite the change of environment due to the Island's natural diversity.
Ack! That's like going up to someone religious and telling them that God is Satan!
Jacob and the "smoke monster" (known by fans as the MIB or Man In Black since the writers apparently never bothered to name him) were brothers, as described above. Though Jacob was certainly flawed, he was the "good guy", for lack of a better term, in comparison to his brother (well, more of what his brother became).
I think the main problem people have with the show is either being overwhelmed or not caring enough about it to try to understand it. Yes, the writers did do some goofy things, and they did abandon some storylines in favor of others. That will happen naturally in a show that lasts as long as LOST did and with changing times and perspectives of those involved. But if you can step back and look at the big picture of the incredibly crazy complex background they created for the show, then the occasional mess-ups in the writing don't matter. It's a show that's definitely not for everyone, but I think people just like saying how annoying and confusing it was because it's popular to say that, and I wish people would see it for what it was.
That's just my opinion, of course.
