I know people have been beating this one to death in the theories and associated comments but I just wanted to throw my two cents in.
I do believe that Mother is a smoke monster, and for the following reasons:
1) The temple seems to be something that would predate Jacob and MIB's birth. In the temple we saw hieroglyphs that picture people worshiping a smoke monster, indicating it was present before the MIB was thrown down the wormhole.
2) People keep saying that it was some power/ability still unbeknown to us that allowed Mother to kill everyone in the camp, throw 200+ Ib MIB on her shoulder and carry him up a ladder, fill in a well with stone and dirt that was at least 30+ feet deep and 3-6 feet in diameter, rush home, grab Jacob, go to the wormhole, pass the torch, and make it back home a bit after the MIB woke up.
This is, IMO, a more major assumption than that of Mother = Smokey. We know that Jacob is quasi-immortal, can heal people, and seems to exhibit some omnipotence. No where has it been alluded to, or shown to us, that he has super human strength, breaths fire, and is faster than Flash Gordon. Therefore, the more straight forward answer, given the information we have, is that Mother posses powers that Jacob doesn't, because she is the smoke monster.
People then say how can she be killed if she is the smoke monster. This is the only damning question to the theory really but we still don't know if the whole "Kill him before he speaks" thing is literal or figurative. It seems all too intentional that the MIB would use the same knife Dogen gave Sayid to kill FLocke with and stabbed Mother before she spoke while Sayid got his stabbing in after a "Hello Sayid".
Secondly we don't know what the ramifications would be of being the island protector and the smoke monster. This could be the answer itself.
And people have also said why would there be a body left if she is the smoke monster. I am in the camp that if FLocke is killed in Locke form, he will die in that form, there will be essentially two John Locke bodies on the island, one real, and one made up of God knows what inside; cameras, cash registers and cigarette ash? The point being if your killed in that form you stay in that form.
3) The dialogue in Across The Sea made it all to apparent, at least in my eyes, that Mother is essentially the personality of Jacob and the MIB combined. Or more accurately I suppose, she raised them to take on a different side of herself, one part good (Jacob) and one part bad (The MIB). I know people will say Jacob beat up the MIB and the MIB felt guilt and regret for killing his Mom and so forth. I am not saying that they are pure good and pure evil but their scales are definitely tipped, to a large degree, in opposite directions.
Now that we know Jacob became the guardian, and MIB the smoke monster. It makes sense to me that both are needed to protect the island. Mother was both, now Jacob took on the guardian portion and the MIB the security/enforcer portion. Just as Mother holds both the white and black rocks in her hands at the end of ATS, now Jacob is the white rock, and the MIB the black.
4) How does Mother know what will happen when you go down the wormhole, how does she know it is worst than death? Her conviction in telling Jacob not to go down the hole seemed to me to stem from direct knowledge. How else would she know? I don't buy that the island guardian just gets uploaded with all these data points when assuming the position. I think she warns Jacob because she did it herself and this is why she says thank you to the MIB when he kills her, she welcomes death compared to what she is now.
5) This is one of the weaker points IMO but people have mentioned how Mother so stealthily descended the ladder to talk to the MIB, they say she entered in smoke form. It did seem like she was oddly quite going down a bamboo ladder but that is all I will say of this point.
The only thing I would accept in rebuttal of this is that Mother just simply summoned the smoke monster to attack the village after finding that the source was compromised, similar to what Ben has done.
Little long I know, just wanted to try and get all the talking points in that I have seen around the site. Thanks for reading.
P.S. Completely unrelated, but isn't Jake a form of Jacob? what if the MIB's name turns out to be John? Someone's probably said that before but oh well.