Back in season 5, when young Ben is shot by Sayid, he is given to Richard who in return states that he can heal Ben but that he will never be the same. I think this has to do with the revival method used on Sayid and also maybe Claire (temple fountain). If this is so, and if the term "will never be the same" means "infected by darkness" - the affliction affecting Sayid currently in the past season 6 episode - then Ben being infected by darkness makes sense. It also explains why Jacob never acknowledged Ben's presence as a leader and never met with him face to face at all.
Secondly, what does this mean to be infected. When the head temple other (samurai-looking dude) runs the tests on Sayid to try and find this infection, he throws that gray powder over him, electrocutes him, and burns him with a prong. Since the samurai dude used the gray powder which is also used to block the smoke monster from traveling places, maybe that means that the infection has to do with smokey. Obviously, it would seem that the smoke monster is bad and Jacob is good (also I hope it's a well-known fact at this time that in the season 5 finale, the black-haired man sitting next to Jacob is the smoke monster). So maybe this points to them both being Gods or maybe Aliens as far fetched as that sounds. But this is LOST, if three seasons ago I proposed the idea of time travel and side-flashes, that would seem equally out there.
As for the other two tests, I have a question: am I the only one who noticed how much Ben gets hurt? And have we ever actually seen him go through pain, yeah he may limp or something like that because of bodily discomfort, but my question is - do we know that Ben feels pain? Because (for one, this would mean that my first paragraph is wrong to some extent) why else would the samurai dude electrocute Sayid amongst other things and then diagnose him as infected even though his reactions on both sides seem normal and reasonable. Maybe people who are revived through this temple fountain the correct way, do not feel pain afterwards, and because Sayid felt the electrical shock and hot metal on his back, that is why he failed the test. Why else would they add needless tidbits throughout the seasons of Ben falling down icy steps or getting beaten up for the thousandth time. It would seem he's careless of pain, maybe because he does not feel it.
Also, last episode the "possessed" John Locke tells Richard that it's nice to see him out of chains. What do you think this means? All of these things point to there being Gods or Aliens. As in the season 5 finale, when Jacob and the smoke monster are talking to each other as the large boat of humans draws closer, they speak of the people as if they are not part of the human kind (as if they are above it). The only extremely unanswered questions with only small leads are: where does the possessed John Locke want to go home to? Maybe his planet and maybe the island is some kind of time-traveling spaceship which he is the security system of. Who knows but what do you all think?