1. The kid was super annoying.
2. Gort was in 2 scenes, and he turned into a cloud of little bugs that ate everything in the second scene, for no reason.
3. The CGI Gort looks totally fake. They could have shot an actor on a green screen and made him look 20 feet tall like Xerxes.
4. Klaatu has magical powers that fluctuate depending on what the plot calls for at any given moment.
5. Klaatu has magical powers, full stop.
6. Klaatu kills people to show how violent and destructive humans are?
7. Life is so precious that the super advanced aliens need to abduct animals on an ark because they plan on killing every living thing on the planet?
8. The super advanced aliens invented a weapon that eats absolutely everything, including rocks, because they wanted to wipe out the humans. Why not just engineer a human specific virus and spare all the other creatures?
9. The alien super weapon can convert any random matter into more copies of itself regardless of the chemical composition of what it eats, and it can apparently generate a limitless supply of energy out of nothing.
10. If the aliens have free energy and they are so worried about humans polluting the Earth why not just give humans the free energy technology and solve the problem without killing anyone?
11. Klaatu makes one half-assed attempt at contacting all the world leaders and then decides "To hell with it," and releases the super weapon to destroy the planet.
12. Klaatu's people are hypocrites, as John Cleese points out. Klaatu's people DID destroy their home world, and in a fit of desperation developed free energy, and instead of giving other species the same opportunity, they decide to wipe them out instead.
13. Klaatu's people can cancel inertia, so why does he need the password to escape the government prison? Why doesn't he just blast his way through the walls?
14. The size of the killer bugs Gort transformed into varies depending on the scene. In one scene they are microscopic, in another they are clearly the size of common garden ants.
15. Klaatu DOES say "Klaatu barada nikto" but super loud "dramatic" music drowns it out.
16. Why did Klaatu's ship land on Earth in 1928 to pick up Keanu Reeves' body and then decide to come back in 2008 to kill all humans when humans were clearly making progress in saving the planet by that time. The worst time for ecological destruction was in the 1950s when thousands of open air nukes were being detonated. Pollution and environmental destruction have decreased since then, so humans are making progress, if at a somewhat slow pace. Klaatu should be able to appreciate that more people care about the environment now than ever before.
17. Klaatu destroys Gort in the end.
18. The device Klaatu uses to destroy Gort not only destroys all electronics on the planet, it stops everything mechanical, whether it is electronic or not!
19. Building on the horror from 18, think of all the people who died when all machines were destroyed? Every plane in the air fell to the ground, all submarines sank and were crushed in the ocean, everyone in an elevator is trapped and will suffocate, everyone on a ship is permanently stranded at sea unless they can paddle to shore, everyone who requires insulin will die now that there is no refrigeration, ALL vaccines and medicine will be wiped out, food production will decrease dramatically, 5 billion people, at least, will die. The annoying kid and the suspiciously attractive scientist will almost certainly die within the year. Rather than saving humanity, Klaatu has pretty much doomed humanity to the iron age permanently, since all the scientists and engineers who will be needed to rebuild the Earth's infrastructure will almost certainly die. It would have been a lot more merciful just to wipe everyone out rather than let billions of people starve to death.
20. WHY THE HELL DIDN'T KLAATU JUST GIVE HUMANS THE DAMN FREE ENERGY TECHNOLOGY?! That would have solved every single problem with the story. None of this makes any sense. That's why changing the story doesn't work. The 1951 story was perfect. "Humans have developed nuclear weapons and rockets and the aliens don't want humans to spread war to outer space so they quarantine the Earth." Works perfectly. The 2008 story makes no sense. "Humans are polluting the Earth so aliens who completely destroyed their home planet with pollution will completely destroy the Earth and remake it without humans." That makes no sense. Just give humans the free energy and no one will ever pollute again! Then no one needs to die! It only takes a few seconds to think this through. The writers could have come up with something just as relevant to the 21st century as nuclear weapons were to the 1950s, but NO, they came up with something incredibly stupid with more plot holes than Swiss cheese! It does not make sense. It doesn't fit. If it doesn't fit, you must acquit.