My biggest downer with the movie was having the alien machines coming out of the ground, and even worse... stating that they had been buried there long before mankind existed! What the Hell was Spielburg thinking? Why would these aliens go to all the effort to plant these machines in the ground before mankind existed, so that they could do battle with mankind to take over the Earth? They already had control of the Earth!!! If they were here first why didn't they just hang up a SOLD sign and call it a day? I was thinking that maybe it was because they were harvesting humans for food, but that would open a real Pandora's box of questions like how did they know humans would develop on the planet (assuming they didn't seed is here)? Or why did Freeman say during the opening voiceover that the aliens had been watching us with envious eyes, which would imply they were after the planet and not the people? And lastly, why did all those aliens digging holes in the dirt apparently survive infection, when according to Freeman the invaders were doomed the minute they breathed our air, drank our water, etc.?
My problem with the ending was how it was led up to. In the original movie, you have the scientist racing to find his girlfriend, and then finding her in the church. Then, as the alien machines come down the street, and the church begins to come apart from the attack, you hear the machines start to falther and crash to a halt. In the new movie, you go right from a nighttime high-excitement, high-spectacle scene of Cruise destroying the tripod, to a bright daylight scene of Cruise walking quietly through the streets of Boston with a dead tripod wrecked into a building. It sure seemed to me that there was something missing in between, and there was no build up to the ending at all. It was like Spieldburg just wanted to wrap up the movie with a "tada... they're all dying of germs - ain't that ironic!" ending in the easiest way possible. He could have gotten the same effect by having the alien commander in his ship looking at a globe and smacking his head while saying "Earth? What the $%&* are we doing on Earth? We were supposed to be on Sigma Alta 5! Oh man, let's get out of here!"
Lastly, the boy should have died. Period. Cruise is standing there as the whole ridge where the kid went is engulfed in flames so hot that all of the humvees are on fire, and only runs towards the farm house after the flames have scorched everything. For the kid to have survived, he would have had to run past Cruise, and Cruise would have seen him. For the kid to show up at the end of the movie, unscathed, was really outrageous.