The Day the Earth Stood Still (2008 film)/WMG

In the remake, Klaatu is an angel.
When he's asked what his original form was, he says "it would only frighten you". But he knows that the people he's talking to are trained scientists, and they would hardly be frightened of an enormous bug or amoeba or whatever. So his original form was something that really would frighten a bunch of rational, agnostic scientists - an angel.
 * You know, that makes FAR too much sense. It can't be correct. ;)
 * There are non-supernatural alternatives which would still scare the scientists. For example, a huge Goatse.
 * Uhh huh, so he's really an Angel? Then where were the DoD's equivalents of the EVAs?
 * The Department of Defense used Reapers and other Unmanned Air Vehicles (those giant remote-controlled planes) for that. The control schema for a UAV is very like that for a mecha; the big difference, besides form-factor, is that they are unmanned. Even this DoD sees that as an advantage.
 * Agnostic is not god-phobic, right? (If you meant atheistic, the answer is no.) And rational definitely is not. Either way, would it not make more sense to have them pick up the angel and start interrogating him while they attempt to discover how his body/brain works/is made of?
 * Finding an actual, provable supernatural being of any kind would fascinate any rational, agnostic scientist. Not that most scientists are either rational or agnostic-- most belong to a religion and they're about as rational on average as any group of human beings.

In the remake, Klaatu is an Eldritch Abomination.
Klaatu is not afraid that he will frighten the scientists by telling them what he is; rather, he is afraid that he will completely destroy their world view and drive them all insane.

Klaatu and the observer go insane after being subjected to human emotion
The observer quickly realized that humanity needed to be destroyed if the Terran ecosystem was to survive, but after enough time spent as a human, he also decides that they're wonderful creatures and would rather die than live in a universe without them. Klaatu reacts similarly, but because he gets more intense emotion over a shorter time, he ends up caring about Jacob personally instead of Humanity as a whole. That leaves him unable to kill Jacob despite knowing it to be necessary, and he decides instead to Take a Third Option no matter how unlikely it is to lead to a good outcome for his own people. In both cases, a sufficiently dispassionate and genre blind observer would call them suicidally insane.

The remake is the beginning of the punishment Klaatu promised if humanity failed to shape-up.
Two Words: Keanu Reeves. Soon, Keanu Reeves will be starring in all of our movies, and this will cause a black hole of despair and destruction that will consume the Earth.
 * Until Bill and Ted arrive from the past to save us all with their message of lighthearted humor and silliness!

Humanity will, just barely, survive the EMP and seek retribution
Think about it. The EMP will cause such widespread global disarray that millions, if not billions, will die. We'd be lucky to retain any level of modern technology, society, and democratic government afterwards. This is going to make people very afraid of the alien federation... and very angry at them. What's more, the only people who know that Klaatu spared us are the scientist woman and her son, who probably will have credibility problems considering they aided and abetted Klaatu.

Fast forward a few centuries after reverse engineering the dead Gort cloud remains, and humanity will start a jihad to make Warhammer 40000 proud against the alien eco freaks. The aliens will never see it coming back to haunt them, either. "Klaatu2: You disgusting machine things are still less than one million times as advanced as us.

Humans: It does not matter. We have devoured the mass of thousands of stellar systems. We outnumber you one hundred trillion to one. Zerg Rush! Zerg Rush! Zerg Rush!"


 * Considering that the EMP would have the least affect on those that don't use electricity in the first place (pre-industrial cultures, Amish, other assorted Luddites, etc.) those groups would both be in the best position to dominate the society that results and have the least reason to seek revenge. If FTL can be reverse-engineered within a few generations, before memory of the attempted genocide fades, a splinter group could try to start up the jihad described above, but Earth as a whole would be unlikely to go along with it willingly. Of course, if the aliens decide to just ignore humanity for several thousand years, the above scenario could still happen without Earth involved.

Klaatu's people trying to stop humanity's destructive ways was a Self-Fulfilling Prophecy
Inspired by the above trope, if humanity had been left to its own devices they would have eventually become a better race and taken care of their earth, and would eventually expand peacefully into space. But now that Klaatu and his kind nearly wiped out humanity, we have a reason to continue being warlike; we need to protect ourselves from them and any other aliens who want to destroy us for not meeting their standards. Since no one knows if and when they will be back, humanity primes itself for defence, and when Klaatu comes back ... there's a very nasty surprise waiting. "Human: "Take this message back to you people." *BOOM!*"


 * It gets worse. The environment's carrying capacity would probably be unable to support even half of our population without modern tecnology. Entire ecosystems will go extinct while we attempt to rebuild because hunger comes before environmentalism.

The movie is the setup for a Steampunk future
Think about it. They EMP everything. But that wouldn't affect things powered by steam. When we rebuild, we will have steam powered tanks, computers, etc.

They should, indeed, give up or blow us all up. It's not like this is gonna be better for the non-humans on the planet than the pre-attack status quo.

The humans will begin to develop biological superweapons that are unEMPable.
They'll eventually end up as something like Prototype times the Tyranids. And since the aliens think anything natural is soooo much better than technology, they wouldn't do more than smile and nod.

Klaatu and his ilk are Anti-Spirals
Well, they're the proto-Anti-Spirals. See, after the horrifying cataclysm that Klaatu caused, Humanity unlocks Spiral Power, and begins the process of becoming a grand empire. The Anti-Spirals don't like that, so they do... what they do; impose a stasis on themselves, attack Humanity, and (temporarily) win.