Everyone goes into a film adaptation of a novel expecting some divergence, and for the most part, Peter Jackson was true to Tolkien's beloved tale and expansive universe when he made the Lord of the Rings trilogy. Even so, there were still some things left out of The Lord of the Rings films, and a few of the lost details are rather massive. While some devout readers hate the LotR movies for these changes, a number of Jackson's creative choices are understandable.
However, some revisions actually make the story more convoluted, leaving one to wonder what went in to those decisions. Most people were probably okay with the omission of the ever-singing Tom Bombadil, but the final battle at the Shire was more sorely missed. Even with over nine hours of screen time, it's amazing how many important details Jackson's LotR trilogy missed, and knowing the full story leads to a better appreciation of Tolkien's genius.
Aragorn's Fellow Dúnedain Descendants Are Missing
As a Ranger of the North, Aragorn's job entails more than just wandering around. He is a descendant of the Dúnedain, an ancient race of men whose purpose is to stalk the Free Lands, smiting evil wherever they can. They are superior warriors, and live three times as long as normal humans, which explains why Aragorn is 87 in the movies, despite looking relatively young.
In the books, Aragorn is the leader of the Rangers of the North, and the Grey Company (a division within the group) assists him throughout the War of the Ring. From The Two Towers on, basically everything Aragorn, Gimli, and Legolas do is supported by the Grey Company, despite their total absence in the films.
The Shire Isn't Taken Over By Saruman At The End
In the movies, the hobbits live happily ever after (for the most part) once the War of the Ring ends, but that's not what happens in the books. Originally, Frodo and his fellow hobbits return to the Shire, only to find it's been overrun by Saruman and his cronies.
They're thrust into the Battle of Bywater, wherein the four returning heroes lead their fellow hobbits into battle against Saruman (who now operates under the name Sharkey). Considering how long the extended cut of The Return of the King already is, it's no surprise Jackson left this bit out. However, he does allude to it with the vision Frodo sees in the Mirror of Galadriel.
Arwen's Brothers Are Nowhere To Be Seen
The movies feature Elrond's daughter Arwen, but there's no mention of the Lord of Rivendell's twin sons, Elrohir and Elladan. Not only are they companions of Aragorn's father, they also work closely with the Rangers of the North (and Aragorn himself) prior to the beginning of the War of the Ring. During the war, they accompany Aragorn through pretty much all of the events of the Return of the King book. These twin brothers stick by Aragorn's side all the way to the bitter end, yet Legolas is the only elf depicted in the film's final battle.
The Ents Don't Go To War During The Entmoot
In the film version of The Two Towers, Merry and Pippin make a concerted effort to convince Treebeard and the Ents that they need to destroy Saruman. Somehow, these ancient spirits of the forest are completely oblivious to the fact the evil wizard is actively destroying their home.
In the film, they hold their Entmoot, but ultimately decide not to go to war. In the books, the Ents are much more willing to go stand up to evil, and are totally down to engage in brutal warfare. Their decision isn't influenced by hobbit coercion, as Treebeard and his allies are already committed to the cause.