Skyline/WMG

The ocean really WAS safe
The aliens have an aversion to being over water. If they would have gotten to the boat they would have gotten to safety.
 * Then again, if you look in the background during the Curb Stomp Battle, the aliens have set four or five naval ships on fire, so apparently they're not that afraid of going over water.
 * Maybe they would get picked up by a nuclear submarine in the nick of time.
 * Seemed to me as if the only reason the aliens weren't over water is because there really weren't any humans in the water, not because of any actual aversion to it.

All of the bio machines they see later in the movie are "run" by characters we have already seen.
Terry, Walt, Ray, whether they are conscious of their actions/former lives or not, they were assigned to the building because they were harvested from there.

Jarrod remained in control of his brain because of The Power of Love
Yes, repeat exposure seems to be part of it, but when he was choking Oliver all Darth Vader style, it was Elaine's voice that got him to stop, and looking into her face made the scary dark veins go away. They are even kissing as the aliens are taking them up to the mothership, so what if there was some sort of brain chemical thing going on under those blue lights?

There aren't really any "aliens" per se' - the invaders are nanotech bioweapons that mindlessly roam the cosmos.
It's a Doomsday Device that got out of hand. Poor earth is just another planet harvested.

Humans Are Bastards + Human Aliens + Powered by a Forsaken Child = Skyline
So, here's this fleet of warmachines that are not only processed by human brains, but also seem to be powered by brains. That has got to be a pretty damn specific design, and there's only a few ways a race with that level of technology could know enough about a human brain to make their machines interface with them THAT well. 1.) They've been here before. I don't like this option, because it means that they'll be here again, but why did they need to come back? Humans can be bred, but there's always the possibility of a plague, cataclysm, shipping error, whatever, I guess. 2.) The aliens are biologically identical to humans, and this is them drafting new units for some war effort. This is how their technology is so closely attuned to our biology and can use it as a processor / battery. Plus, it's a lot easier to justify a questionable military technology to the local populace when you can tell them it's another planet being razed for the resources. It isn't their people getting slaughtered, and they have a war that needs to be fought, so it was an acceptable option, because humans are bastards even if they're not from Earth.
 * Its more likely that they are just powered by brains, not human brains in general, and the brains of other sentient species in the universe are all broadly similar enough that they all serve this purpose, assuming that they don't simply adapt to whatever species they are dealing with.
 * Here's a variant theory. What if the aliens weren't here to invade, but to communicate, the initial abductions simply a matter of study and working out a way to facilitate communication between species? Every human character we see in the movie is basically a shallow, reprehensible dick. And let's face it, the world is full of dicks. When the alien machines absorbed human brains to function as processors, they also became assholes, leading to a peaceful alien mission with a bit of Blue and Orange Morality rapidly becoming an invasion due to their technology running on the brains of jerks. Humans Are Bastards directly leading to Aliens Are Bastards.

Skyline takes place in The Matrix universe.
Think about it - there is no logical reason for the programs of the Matrix to have billions of humans laying around in a virtual world... unless they are actually aliens using our minds to power their war machines. (Makes more sense than using our bodies for heat.) The apartment the characters are in is simply a holding cell for various captured humans - they THINK they're in the real world, but they're not. It's why

The big aliens are Agent programs - they only showed up when the characters tried to leave the apartment. If the characters had been gotten to the building's boundaries, they would have realized they were in a holding area and that there was probably no way to reach another building, let alone the marina.


 * So this could also be a prequel - "the day they took over". Maybe Jarrod is the machine who eventually allows the humans to establish Zion.

Skyline is a big paid ad for Mass Effect 3
Tentacled eldritch aliens are harvesting humans, striking every major city on Earth, and then render their bodies into generic paste after scooping out the brains to power bio-organic husks that glow blue.

The aliens are protecting the galaxy from a dangerous threat and are using humans to help in the fighting.
The aliens are a race that, once they explored the galaxy, discovered a horrible threat to all life in the galaxy. They begin fighting back, but take such heavy casualties that they start using drones to do the fighting. The drones are programmed to seek resources from compatible worlds, and thus come to Earth when their supply of CPUs starts to run low.

The aliens are Phyrexians.
They share the same aesthetic and the same assimilation goal. Their ships even seem to Planeswalk and regenerate.