As for the who's good and who's bad, I think it was a little ambiguous at first but last night's episode really cemented the answer, at least to me, within the final scene. Given what the writers told us in the scene with Jacob and Richard and the wine bottle only to have MiB break it in the final scene pretty much put a stamp on where Jacob and MiB are on the scale of good and bad, although they do tend to blend into shades of gray every so often.
At the risk of sounding dumb, can you -- or someone -- explain to me that wine bottle scene and the metaphor of which you speak? LOL
We were given a story by a character that is believed to be true, i.e. Jacob's metaphor with the bottle of wine. However, the writers then gave the audience a reassurance that the said metaphor was true by having another character illustrate the metaphor, to a degree, without knowledge of the metaphor, in this case MiB smashing the bottle.
Maybe when I first watched it I was too tired to grasp the full meaning. Either that, or I'm a bit dim (I'm sure my wife would choose the latter).