The plot and story were almost completely different than the original due to the dub script changes and the omission of various scenes.

Some bits of nudity and violence were originally edited out by Harmony Gold, and then restored by Streamline. However, the scenes they belonged to were still missing. Here's an example:

Japanese version:

Princess Ahanas is in bed, stretching herself awake (brief nude scene here). Her servant asks, "Princess, will it be the usual today?" Ahanas replies, while wrapping a sheet around her, "Of course! I just can't wake myself up without jumping into the sea."

English version:

Brief clip of Ahanas stretching while voice-over attempts to explain the plot.

Voice-over narration was added throughout the movie where there was none in the original. This included an attempt to give a relatively happy ending to what was originally a tragedy.
This is like ending Grave of the Fireflies with a voice-over from Seita where he says, "Yeah, I died, but eventually I got better."

The original soundtrack was removed, and replaced with a new soundtrack that, while borrowing some selections from the original, was completely different. Akino Arai's (Macross Plus, Record of Lodoss War) vocals removed.

The plot was rewritten from scratch. It really seems like they watched the original version with the sound turned all the way down, and made up their own plot to go with the pretty pictures. The plot in the English dub has nothing to do with the plot in the original. Here's an example:

The original version's plot:

Two pairs of young lovers become embroiled in a war between two rival kingdoms, the primitive but resplendent Isa and the militaristic but undisciplined Paro. Izu and his young wife, Mari, are simple farmers who live in the unassuming village of Saki, which lies directly between Isa and Paro. While Saki does not have the beauty of Isa nor the war machines of Paro, they do possess a magnificent tree known as "Windaria," to which the villagers give their prayers in return for "good memories." When the war erupts, the well-meaning but exceedingly naive Izu sees a chance to grab his five minutes of fame, and perhaps a few riches to boot. Although begged to reconsider by Marin, Izu decides to join Paro's army, enthralled by the fantastic motorbike "given" to him as a bribe. Before he departs, they each take a vow: He will definitely return to her, and until he does, she will wait for him. The other two lovers are Jill, the prince of Paro, and Ahanas, Princess of Isa. They initially want nothing to do with the rapidly escalating conflict, but after Jill's father, Paro's king, dies by his son's hand in an altercation over the war, Jill has little choice but to realize his father's final wish: the taking of Isa. The only problem is that he had promised his beloved, Ahanas, that he would not become involved. Meanwhile, a young woman named Dorido awaits the return of her lover, a man who has left the land of the living to become the captain of a ghost ship that flies around collecting the souls of the newly dead.

The English version's plot (from memory):

The evil empire known as The Shadowlands is jealous of the country of Windaria's abundant fresh water supply, and starts a war. A woman (Dorido in the original) went insane when she drank Shadowlander water.

• Currently the only way to get the complete and uncut Windaria is by obtaining an import version from Japan (should be available on assorted home video formats from various sources).