Consider the following: Early in the film there's a discussion on determinism versus 'randomness.' The thing is, in modern physics, quantum physics to be precise, there are certain things which cannot be known deterministically, such as whether an electron will show up with up or down spin in a certain case, or whether a photon will pass through or reflect off a glass pane. These random events cannot be predicted, and thus create uncertainty in the future. However, things can be predicted to be possible, and even probable.
What if, rather than the saviors these apparently angelic beings try to appear to be, they are instead looking ahead, seeing a possible way that things could come about, and then ensuring they happen that way? They knew there was a possibility that the sun would fry the Earth with a solar flare. Let's not get into how ridiculous that is, for starters. But since that flare was caused through a series of quantum events, there was always a chance it would happen earlier, or later, or aim in a different direction. Any number of things could have happened differently.
Yet, these Watchers apparently let the holocaust of Earth happen, rather than prevent it, and they only took a small sample of genetic sources off the planet. With a knowledge of quantum mechanics that advanced, they could have stopped the solar flare from hitting Earth in the first place. Instead, they apparently decided that the way they predicted was the only way things could happen, and forced it to happen that way. Nice job breaking the Earth, 'Angels'. Or maybe they're not what they seem to be.
- Trust me, you aren't alone.
- And even if they genuinely couldn't prevent the solar flare, what the hell was stopping them warning us in plain English, and maybe giving us a few pointers on propulsion systems and terraforming so we could do something to save ourselves?
I didn't check The Other Wiki, so I don't know whether this was already denied by Word of God. Now, let's come to the point. The girl prophesied the shit will hit the fan, and where to go to get saved (possibly knowing it'll only help her granddaughter and new buddy of her). Now jump forward these forty or how many years. Some aliens discover Sun is just about to go KABOOM: "Holy sh*t, what do we do!?" "Well, we ought to help these creatures... Find them a nice new planet or whatnot" "How? We don't have enough ships!" (for whichever reason) "So let's just take, like, some of their younglings, and yeah...".
- It seems that the aliens/whatever were the ones who communicated the prophecies to her - she was hearing the same sort of "whispering" the two kids did. And really, how small is the spaceship that they can't take the kids father along?
- Remember how Nichola Cage's character drank in the first part of the movie. Clearly the aliens took an invisible scan of the father's liver and decided that he wasn't long for this world anyway and rejected him.
After the death of David, the robots realize there are simply not enough specimens - robotic or human - to teach them about humanity.
Searching their research, they devote thousands of years to the idea of alternate universes, and find a way to cross over to a time-stream where humanity still exists. They succeed - only to discover that the sun in this universe is outputting massive flares that will eventually destroy humanity.
They know that Humans Are the Real Monsters from their own timeline; therefore they are unwilling to save all humans. However, they decide that saving a small population of children to seed a habitable world, will allow them to study humanity without the risk of being overrun by possibly robo-phobic humans.
Hence the actions that seem scary and horrifying to the humans - they have their own agenda and saving all of humanity is not one of them. And the "accidents" that occur within the 50 years of the movie is their way of "studying" humanity.
- Nic Cage. That's all.
- The kids are still entering a session. The aliens are First Guardians.