There are biblical references to God sending two angels to Sodom and Gommorah to set tests and pass judgement on the cities before he destroys them (starts with God asking them to find 50 good people, then 40, 30, 20, 10 and eventually they can only find one (Lot) and he and his family are spared from God's wrath).
Now what if Jacob and Nemesis were sent to earth a couple of hundred years ago and were given the island as a kind of paradise where they could test man, and they have been doing this through various groups like the crew of the Black Rock, Dharma, Flight 815 and even before that (see the dialogue between Nemesis and Jacob at the start as they look at the Black Rock in the distance). Jacob believes that mankind are worthy of being saved, where as Nemesis believes they have failed so many times that they have the proof to go back to God to say that mankind needs to be wiped out but can't until Jacob agrees with him, that is why he hates Jacob so much and wants to kill him.
To further this theory I believe that the island is going to be a Garden of Eden where society can begin again after God's Wrath and that Jacob is looking for the right group of people to settle there and form this new society, hence the statue of Taweret who is there to guard the fetility of the island inhabitants that will repopulate the island and restart God's mankind experiment. I believe in Season 6 we will see how Nemesis destroyed the statue at some point after Dharma arrived in the hopes that this would scupper any of Jacob's plans, no kids = no society = no future for mankind and he can go home. When this doesn't even stop Jacob (who uses Dharma to try and find a way around the fertility problem) Jacob finally puts in place Plan B to rid himself of Jacob (The One Who Will Save Us All) and manipulates Locke and Ben throughout a number of decades so that he can find his loophole to go home, not his loophole to kill Jacob (although it ends up being one and the same).
The questions this leaves is why Jacob so willing offered up his own life (he must have known Ben was at breaking point and saying 'What about you?' would push him over the edge) and who 'They' are when he says 'They're coming', because I'm not convinced he was talking about the returning 1977 Losties (note the genuine fear on Nemesis's face when he says it). I do think Nemesis is the more evil of the two (although I'm not convinced either are evil) due to the final shot we see of Nemesis and Ben as the flames (of Hell?) licked up in front of them.
Also, how awesome an ending to the TV show would it be (at least visually) for all of humanity outside the island to be purged in much the same way Dharma was purged by the Others after they had proven themselves unworthy inhabitants of the island?!
) as it would make what the nemesis at the begin said make sense - ie they come fight kill and corrupt. However i cant say i like the overall theory...