Battle: Los Angeles/WMG

The aliens are the Tau
The aliens, and a Tau Fire Warrior. Note that, A. they are both yellow-armored military aliens with B. a fondness for More Dakka and C. similar helmets. They both have legged walkers as transportation and assault drones. Although the Tau have different colored skin and blood, in 38000 years, they might have changed somewhat.
 * The Tau aren't aquatic, the aliens wear neither helmets nor armor, and the Tau hadn't even invented fire in M2.

The aliens are desperate.
If the ARG is to be believed and the aliens really have another thirty million soldiers heading in, it's a little odd that they bothered with their initial assault at all; at the very least, they would be able to march troops up and down more of the coastlines of the countries they're hitting rather than just taking a few major cities. The oceans shouldn't even be much of a bottleneck, since they use existing sewers and canals to funnel water behind the frontlines so they can use it to resupply. They've either done enough recon to expect that this infrastructure is in place or they took a glance at Earth from above and figured this infrastructure would be in place based on our level of development.

If they need water so badly that the ocean level drops in less than a day, it may be safe to assume they're on their last legs (or tendrils.) The Marines notice that their rifles are surgically attached to their arms, one going so far as joking "now that's commitment to the cause." They're clearly not a Hive Mind, but they could be a society driven to military dictatorship due to scarce resources.

This could be why the aliens, despite their advanced technology, are not invincible; they've lost much of their own military capability due to lack of resources and much of their population in their own resource war before finding Earth.

Corollary: a future installment will address the problem of astronomers discovering a multitude of water-covered planets in the galaxy not by taking the obvious way out of saying that the salt content in Earth's oceans are what makes it attractive to the aliens, but by having the aliens be so desperate that distance was the deciding factor and Earth was simply the first one they found. Peace is brokered with an exchange of this information so they can go find other fuel sources. Unfortunately, it turns out that they didn't have the patience to look further than Earth because they're already at war with something even worse and losing; to add insult to the invasion, humanity can choose to either watch the invaders get curb-stomped only to be destroyed next, or suck it up and form an actual military alliance with the original invaders to give them the manpower they need to rout their own enemy.


 * Adding to this, this may help explain why their tech looks and acts the way it does. Their weaponry and vehicles look very roughly-designed, almost as if they're partially cobbled-together.


 * Jumping off of that. They could have been a colony ship or something that was forced by some circumstance to act as an invasion force, forcing them to MacGyver all their soldiers, weapons, and equipment from scientific, mining, or other colony building equipment. That would explain why they would have a good understanding of basic combat tactics, as any advanced civilization would have to have some concept of combat, but didn't just overwhelm the humans. They are technologically advanced and hardly stupid, they obviously learn quick, but they simply aren't battle hardened.

This movie takes place in the Ijiverse
The Aliens aren't resorting to the Alpha Strike yet, but when they do...

Earth is the highest-technology level civilization they have ever encountered - or at least fought.
They've mowed down many a stone age level and medieval level civilization - something that their legged-tanks would be pretty formidable against. They're fighting someone they can't roll over as easily as the did before.

This is their first large-scale land attack.
There's plenty of water worlds out there, and that's what they usually decimate. They just usually have little in the way of land to worry about. Fighting on land is new to them (or it's just been a really long time), but as the first WMG says, they're desperate and had to pick a 70% water planet rather than a safer 90% water planet with water-based intelligent life.

The aliens assumed skyscrapers were command centers
The aliens seem to be beating the snot out of the buildings in downtown Los Angeles - this is because they don't realize that those buildings are for business and residential usage and not for government. Their own command center is centralized in a large structure so they assume ours is too. A disproportionate amount of their forces are clearing and destroying these buildings, which helped the film's protagonists in the end.
 * Fridge Brilliance. Many skyscrapers are used to broadcast TV signals, so in a way they were. Much in the way we tracked their C&C center by it's strong RF signals, it's not unreasonable to think that in a big urban center a skyscraper with a powerful TV antenna on it might be one of the most powerful obviously artificial electromagnetic signals to be found, and therefore not a totally illogical target.

The alien being dissected was able to send out a distress signal
As they are ripping the still-living alien soldier apart to find the weak point, a squad of aliens immediately heads for the police station.

The aliens don't just need water, they need salt water
The Kuiper Belt and other cometary material in the Solar system contain much more water in toto than is found on the surface of the Earth. If they just needed liquid water, they could break off chunks of (say) Pluto, and melt it. The reason they're so interested in Earth is that our ocean water has a mix of salts in it that provide just what they need to use water as a fuel. (There isn't very much sodium chloride in comets, to name just one kind of salt in Earth's ocean water.)
 * Fridge Brilliance?

The aliens are using an inefficient implementation of a hydrogen-boron fusion reaction.
They electrolyse the necessary hydrogen out of the seawater and then strain the small amount of available boron from the remnants while stockpiling all the hydrogen they can't use. Then they use the hydrogen and boron that they have to power their land offensive. This offensive is both to clear a safe zone and to find places where the C&C units can burrow into the earth and begin extracting boron deposits.

The aliens have to refine/filter/whatever the seawater before using it
Just like oil is refined for various uses, the seawater is refined according to each use the aliens can apply it to. The "command center" isn't just command, it's a refinery. This is why it took the aliens a while to get their vehicles and air units up and going.
 * If they were taking deuterium out of the water that would make sense.

The government knew someone was coming, but not much else.
They didn't have the time for it to become a Government Conspiracy, but astronomers could see something was coming and alerted the government. No one knew if it was friendly or hostile, and they only had a few weeks before it was due to arrive - so all they did was make sure all military bases were stocked up. With so little lead time, it was better to set up a small committee to chew on both options rather than mobilize and tell everyone. This explains how they obtained the recon photos of the landing modules - they were ready to take the pictures.

The aliens never really developed the wheel as a mode of transportation.
I'm sure the understand the concept of the wheel and all, have gears, etc. However the two legs on the tank-thing are a little odd. It obviously works for them, though.

The Aliens are just getting started...
What we saw in the movie was simply an advanced force of cheeply manufactured Shock Troops. The aliens we see already show signs of being cloned-Shock Troops, weapons grafted to the arms, being hard to kill, etc. Here's the strategy: the aliens send off these Shock Troops as an advanced force, complete with cheaply made drones for support, to a planet to weaken the defenses/gauge the strength of the natives. What we're not seeing is the massive fleet hiding behind Mars.


 * The initial invasion is an army of misfits, not clones. If they are desperate refuges from a Crapsack World perhaps the first wave is convicts, political dissidents and lower tier troops. The kind you could send to die on a low tech planet just in case it's a Death World. Hence the cobbled together tech, cybernetic weapons and the drones. The cybernetics could just could be how they fight. The aliens has medics and in some scenes they'd drag fallen comrades to safety (clones wouldn't necessarily need to do that). Since we found their weakness, they next wave is the Elite Mooks.

The aliens are refugees from a Real Time Strategy game
Think about it: They have an initial base, but start off with only basic troops. They have to collect resources before they start putting out more advanced units like aircraft and walking tanks, and they instantly lose when their base is destroyed.

The aliens think humanity is a threat
Humans have so many tall buildings, whereas the aliens only have a few of those kinds of things. Humanity must be some kind of existential threat! It's time to invade with the army they have, not the army they want! As for WMDs, well, the aliens apparently were never in a situation where they would need to invent such things.
 * This makes sense to me. It seems entirely possible that the aliens are xenophobic or scared enough to try and wipe out any advanced species they encounter (Or maybe they just watched Starship Troopers too many times) and the reason the water drops so quickly is it just happens to be a convenient fuel resource for the aliens to use in an effort to exterminate the extremely violent and aggressive natives. It's not a standard invasion so much as a poorly thought through act of panic. I would also laugh hysterically if the sequel said the whole war was all Paul Verhoeven's fault.

There really are no other planets with liquid water near Earth in the B:LA 'verse...
...because the aliens have already drained them dry.

The alien that came up out of the pool again was named its language equivalent of "Mario"
Super Mario 64 reference - when Mario is low on health he can jump into water and then come back out with his health refilling - due to the breath meter being the health meter. This alien used the same thing!

Each command center included one actual alien, everything we saw was a drone.
The air drones were entirely mechanical, and the troops were biomechanical clones (Much like the clone troops in Star Wars). Earth is actually being invaded by a very small but incredibly well armed group.

The movie is set in the same universe as Sora no Woto.
Or rather, the film is a distant prequel, showing the beginning of Mankind's war against the alien "Them." Over several years, Earth unites to fight them off and eventually succeed in doing so. But by then, the aliens had drained a large chunk of the planet's water, civilization is largely devastated and the scattered civilian and military remnants find themselves stranded...leading to the creation of Helvetia and Roma.

The Aliens are the fleet that Chris got when he left earth in District 9
Tell me I'm not the only one that thought this. There are only two things that go against this theory: The Marines are very obviously surprised by the presence of Aliens, and the aliens in District 9 didn't seem to have any preoccupation with water.