Ok, I have a few ideas on the subject. Good call on Ninos part that the funeral parlor was in a predominantly black neighborhood, that no one showed up to. I think it was Michael in the box.
Also, I don't think Naomi's boat causes problems. People refer to the future Jack as a hero, not 'that dude who saved 2 people, and got 38 other 815 survivors shot dead in the process.'
I think Jack telling Kate 'he was right, we need to go back' or whatever is the result of Ben asking Jack why he wants to leave, what he's really going back to. The maps and all in Jacks apartment are his attempt to find where the island is. It's possible Jack thinks if he stayed on the island, he could have learned some of it's secrets, like the advanced healing. I don't think he's taking drugs to kill himself to get back to the island, I think he's taking drugs to cope with severe depression from leaving the island, and he developed a dependency.
I think Jacob can take the form of anyone to anyone. I think when Walt appeared for Locke, Eko's brother for Eko, and other non-descript encounters, it was all Jacob. Who or what Jacob is, exactly, is still a mystery though.
I don't think Locke's father was not Jacob. This was not a non-descript encounter, Locke's father knew details of past events, so I think it was actually him, but how he got to the island, I don't know.
Remember when Locke and Ben were going to see Jacob, and they passed over a line of sand, that Locke took note of? I think it was the cloud monster, lying dormant. I think it's another tool that Jacob employs, that Ben knows about, but lies to the Others about.
As far as Naomi, I think she works with a competitor of Pennys fathers company. I think they had a mole in that company, and got wind of Pennys search for her boyfriend, at the center of a large magnetic disturbance, like we saw at the end of the second season, and went to go look for the island. She had the picture of Desmond and Penny so that when she found Desmond, she knew she'd be in the right place. What exactly they think they can find there, I'm not sure, but I think to researchers in the real world, the magnetic disturbance that happened when the hatch blew up was of a pretty substantial magnitude.
I hear future seasons are going to deal more with the islands natural inhabitants, the ones who constructed the 4 toed foot statue. I think Jacob has a strong connection with the islands natives, and that's how he can do what he does.
Edit: Now I'm thinking about it, so I have more stuff to say. I think Naomi's boat will come to the island, and get stuck there. When Desmond tried to leave on his boat, he couldn't, for whatever reason. I think Naomi's people will work with the 815 survivors, fighting the island natives, and eventually, Jack will figure out the system that got Locke's father to the island, and reverses it, to get everyone off of the island.
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