Last Order Differences

There has been given no reason as to why the changes were in fact made. We only know that Square-Enix actually did not make the film, but they had to OK it for release on the Advent Children DVD.
The most common reasoning with the fans is the fact that Cloud has some serious issues with the truth of what happened in the game. I even wondered if, when Tifa was helping him sort it out in the Lifestream, that he was actually telling the truth then. If this is the case, then all the differences can be just shrugged off. The way I look at the film, is this is the way the events actually happen to Cloud and Zach.
Here are all the differences there are between the two:

As many fans would know there are several differences between Final fantasy VII, and the Last Order: Final Fantasy VII. Here are a few
In Final Fantasy VII, it shows Tifa's father already dead inside of the Mako Reactor.
In Last Order, she finds her father dying outside of the reactor. There is also some dialog between her and her father in Last Order.

In Final fantasy VII, when Cloud attacks Sephiroth in Jenova's chamber, Sephiroth turns and is stabbed in the stomach.
In Last Order, Cloud stabs an unsuspecting Sephiroth in the back, before he is even aware of Clouds presence.

In Final Fantasy VII, Cloud shows Tifa he is knocked out during the fire at Nibelheim.
In Last Order, Cloud is told to help Zangan get survivors out of town, then he goes to the reactor.

In Final Fantasy VII Cloud is stabbed by Sephiroth one time.
In Last Order, he is stabbed by Sephiroth twice.

In Final fantasy VII when Sephiroth leaves with Jenova, Cloud gives pursuit to the catwalk above the shaft. Sephiroth turns, stabs Cloud, and dangles him over the shaft. Cloud Pulls out the blade, and throws Sephiroth into the shaft with it.
In Last order, Cloud charges Sephiroth in front of Jenova's chamber, and is stabbed the first time. He then tosses Cloud into the catwalk, and there stabs him again. Sephiroth hoists Cloud above the shaft, where he pulls the sword into him, and throws Sephiroth into the wall. Sephiroth then jumps into the shaft himself.
*Note* The events of this that take place in Last Order, also are the same as the events of Crisis Core.

In Final fantasy VII, after stabbing Sephiroth in Jenova's chamber, Cloud moves Tifa. There is no dialog present between the two, thus corroborating the fact that Tifa has no memory of Cloud being there.
In Last Order, when Cloud moves Tifa, she becomes conscience, and there is some dialog.
This is perhaps the worst change they could have made. It is a major plot point of the game, especially the fact of Tifa having no memory of Cloud being there.

In Final Fantasy VII, when Zach finds Tifa wounded, he just checks on her before continuing.
In Last Order, there is some dialog between them, before he goes after Sephiroth.

In Last Order, there is dialog not present in Final Fantasy VII when Cloud and Sephiroth fight.

In Final fantasy VII, the battle between Zach and Sephiroth is about 2-4 seconds long.
In Last Order, the battle lasts at least a full minute.

In Final fantasy VII, Zach puts Cloud in a SOLDIER uniform.
In Last Order, Cloud is still wearing his original uniform throughout the entire film.

This last one is not really a difference, just something to point out. In Final fantasy VII, it shows that Zach and Cloud are ambushed by Shinra just outside of Midgar. Zach is killed, and Cloud is left for dead.
In the end of the film, you see Zach getting in front of a bullet meant for Cloud. Then the film ends, and you hear Zach say "Cloud!...Run!"
It is thought that this shot, which was not seen in the game, is the reason Zach could not get away. It is entirely possible, but we will not know for sure, until the release of Crisis Core: Final Fantasy VII.