A few things...
"Mother" was obviously the previous guardian (i.e. like Jacob) - let's not assume she's a smoke monster just because she's a mass murdering maniac. Just because Jacob didn't show any super powers except immortality and the ability to grant it didn't mean he didn't have any. The same would apply to his mother too.
Also - note the "ritual" she used to transfer... or maybe "share" guardianship? That's the same thing Jacob did with Richard... I wonder if there's something Richard isn't telling us.... or maybe something he doesn't even know.
As for the black/white/good/evil thing... I'm starting to think Smokie isn't the "bad guy" in this. Jacob keeps him on the island, keeps bringing people there to die, keeps messing with people's lives...
As for the wheel thing... that was a bit weak, but keep in mind, the people there had 30 years to play with things, and obviously approached it from a mystical, rather than scientific POV... which the "rules of lost" seem to favor...
Since "Mother" destroyed everything/one before it could be built, I guess it was built by people jacob brought to the island.. odd.
Oh yeah, one more thing... about MiB being able to kill the mother before she talked... keep in mind... Smokie told Richard to do the same thing to Jacob... so...