The ending, where a now-adult Walter goes back to the uncles' farm to pay his last respects. Not long after he arrives, a helicopter lands and a clearly rich Middle Eastern guy steps out. It turns out that the Sheik was his grandfather, and he'd been raised hearing stories about the uncles. For all the money and power he had, this guy is just so happy to find out that his grandfather's stories were true.
Sheik's Great Grandson: So, the two men from great grandfather's stories, they really lived?
Adult Walter: [wistfully] Yeah, they really lived...
The original ending takes it even further, and has the thugs that Hub fought earlier showing up, now reformed and respectable people.
Further than that, besides the thugs, there's an entire detachment of MOUNTED French Foreign Legionaries with riderless horses as an honor guard, and not the Sheik's son but the Sheik himself, an elderly man with an eyepatch and an oxygen tank who arrives with his harem to pay respects to his old adversaries. The director apparently decided the whole thing, including introducing Adult Walter's wife and sons, was too much for the last five minutes. Thank goodness for DVD extras.
Hub: Sometimes the things that may or may not be true are the things a man needs to believe in the most. That people are basically good; that honor, courage, and virtue mean everything; that power and money, money and power mean nothing; that good always triumphs over evil; and I want you to remember this, that love... true love never dies. You remember that, boy. You remember that. Doesn't matter if it's true or not. You see, a man should believe in those things, because those are the things worth believing in.
Doing the art for grown-up Walter's comic-strip studio inspired Berkeley Breathed to take up cartooning for real again after an eight-year retirement.
If I hadn't had so much fun drawing these fake comics, it would never have occurred to me soon afterward that I should be drawing the real thing again. Life imitating art, as it should be.
Minor one, but the teenagers that Hub beat up earlier. First off the McCann Brothers were polite enough to take them to their house to ice up their wounds with cold meat. Second when they heard that there was a lion on the loose they along with the McCann Brothers and their golddigging relatives decide to arm themselves to rescue Walter. He wasn't in danger but it's the thought that counted. Last they listened to the entirety of Hub's Speech about how to be a real man. To take it Up to 11, the deleted ending shows that they took Hub's words to heart and became respectable men. They even have the heart to show up at the funeral.
Two words: "Welcome home."
The relationship with Walter and Garth and Hub. Garth and Hub stated before that they don't know nothing about kids and don't like kids. But they gradually warm up to Walter and enjoy having him around. When he leaves with his mother, they are genuinely saddened, Hub even suggesting they use the money they have left to fight Mae for custody.
Mae was willing to let Walter leave her when she realized that he was right and that was best for him. Even if her actions in the movie were by no means completely redeemed, it shows that at the very least she is aware of how terrible a mother she has been and that Walter's uncles can give him a much better life then she ever could.