What Spielberg, Cruise, and Koepp accomplish here in the first two acts is nothing short of revolutionary. They've made a big-budget summer blockbuster about massive destruction and action that manages to studiously avoid every cliché and expectation of such films. It stays resolutely on the characters' points of view, showing us almost nothing they don't see, even to the point of coming tantalizingly close to a raging battle, then avoiding showing it. It keeps its focus on character instead of spectacle. The "hero" of the piece remains decidedly unheroic, wanting only to escape, and trying to talk others out of fighting back. The purpose of every piece of action is to frighten and disturb rather than thrill, making ingenious use of familiar 9/11 imagery. At the end of the second act, it is hands-down the best alien invasion film ever made, and perhaps one of the best sci-films of all time.
Then something strange happens. The filmmakers lose their nerve, and remember that this is an extremely expensive summer film financed by two studios. Or perhaps it was the fact that it stars Tom Cruise, who up to this point has spent almost two hours doing nothing but run for his life. Suddenly, and tragically, the film changes, violating not only its carefully established tone, but its own internal logic. Suddenly, Cruise begins to act like a hero, and summer action clichés force their way into the story like a worm into an apple. The transition is jarring, and it creates a serious disconnect from the story.
While it's true that Wells' original ending creates a problem for a movie, here they try to remain faithful to it, while still shoehorning moments of triumph into the conclusion. Unfortunately, these moments come off as alternately false, unbelievable, and meaningless, since it isn't mankind that defeats the invaders in the end.
Is it recommendable? Well, I suppose that depends on what kind of viewer you are. If you feel that 75% brilliant material overshadows the 25% that falls apart, then you'll enjoy it. If, however, you're the kind of viewer who feels that the final impression a movie makes is its ultimate stamp on your memory, you may be in for a crushing disappointment. On the other hand, if you're the kind of viewer who just likes the cliché of the boom-boom summer action spectacle, you're likely to be bored and frustrated with the first two acts, and only engage in the end. It is confused about what audience it's trying to reach, and consequently, isn't likely to satisfy any of them.