People may remember that there are two versions of the very first Pocket Monsters movie (Mewtwo Strikes Back) in Japan:  the regular version that was released in theatres and VHS, and then a second version that was released on DVD in Japan and was used as the video source for the English version.  The second version added a number of digital effects and CGI graphics to the original film, all of which were done by the Japanese producers.

Well, it seems that history is repeating itself.  Like the Mewtwo movie, there are two versions of the second Advanced Generation movie, "Rekku no Houmonsha Deokishisu".  One version, which I'll call "the original version," was the version shown in Japanese theatres and is the video source for 4Kids' dub of the film.  The second version, with about two dozen visual edits ranging from recoloring scenes to redrawing characters, was the version released on DVD in Japan.  So, in essence, the Japanese DVD release is an edited version of the original film.  It's sort of how there are two versions of Star Wars:  the original film that premiered in the 70's, and then the Special Edition version in which George Lucas went in and added all these digital effects to make the movie closer to his original vision for the film.  And, similar to the way Star Wars fans can't get the original version of the movie on DVD, Pocket Monsters fans in Japan can't get the original version of the Deoxys movie.

What follows is a list of all the edits that I was able to spot.  Because the "original version" that I used for my comparison was the dub (and the Kids' WB! dub at that), the accompanying screenshots won't be of a very high quality.

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Visual Edit #01
A rainbow is taken away from the scene with Arbok during the opening segment.  

Visual Edit #02
The shot of Deoxys' comet hurtling through space has some colors taken away.  Originally, there was more color, particularly the color purple.

Visual Edit #03
About a week or so before the movie was set to premiere on Kids' WB!, a preview video clip of the movie was posted on the Kids' WB! website.  I watched the clip, which featured Deoxys' introduction into the movie, and noticed that there was an edit.  I posted my findings on the various message boards I visited, and it wasn't until later that I found out that the Japanese version was actually the version edited.

In the original print of the film, we could see Deoxys clearly as it emerged from its meteor.  However, the Japanese DVD covers Deoxys in shadow, shrouding the pokemon's identity in secrecy for a few seconds.

Visual Edit #04
A sign in the upper left-hand corner of the screen is altered on the DVD.  Originally, it read "LaLuze" (a romanization of LaRousse), but on the Japanese DVD it's been changed to read "B-T  Garden."

Visual Edit #05
When Haruka is getting her picture taken by the block robot, the word "SHOPPING" in the background is replaced by the word "SHOPPING"...in a different font.  

Visual Edit #06
When Haruka is walking with her passport, upset over the picture she took, her eyes are repainted black for the DVD.  Originally they were blue.

Here eyes are also repainted when Takeshi starts hitting on Hitomi as everyone introduces themselves to one another.  Interestingly enough, Masato's eyes are left unaltered.

Visual Edit #07
At the Battle Tower, Shouta commands his Kamex to use Rapid Spin.  In the original version, the ground underneath Kamex is blue; in the Japanese DVD version, the ground underneath Kamex is red.

Visual Edit #08
Throughout the entire sequence of Toh'i helping Minun out of a trashcan, the cobblestone street that everyone's standing on is altered to make it look more like a brick-covered street.

Video Edit
During the insert song, there's a close-up of Toh'i turning the jump rope.  However, depending on the version you watch, he's turning it a different way:  in the original, he turns it counterclockwise, while he turns it clockwise on the Japanese DVD.

Visual Edit #09
As Rayquaza arrives in LaRousse, we see a fully-colored Rayquaza flying.  The Japanese DVD was edited so that the first few seconds has the pokemon shrouded in shadows.

Visual Edit #10
This one's odd, because it does the opposite of what's been done before with Deoxys and Rayquaza.

When Rayquaza's image is brought up on the main monitor (inside the LaRousse defense center), the image of Rayquaza is actually made more clear (and not less clear, as the other edits in the movie have done) in the Japanese DVD.

Visual Edit #11
As Yuko runs up to the control room (in the dub, it's when she says "Professor!  How could a Rayquaza be coming here?"), the image on the top center square of the nine-panel display is altered.

Visual Edit #12
As Deoxys is brought up on the monitor, the image is blurred out for the Japanese DVD.

Visual Edit #13
As the city's evacuating, Yuko looks over to Professor Lund and says "Tory's out in the garden."  In front of them, on the computer monitor, is a map of the city.  There was a square there originally, but it's taken out in the Japanese DVD.  In addition,  the windows displayed on the screen are rearranged on the Japanese DVD.

Visual Edit #14
Whenever Rayquaza slams against the forcefield in the movie, there are a great deal of  computer lighting effects added in the Japanese DVD that weren't there originally.

Visual Edit #15
This edit makes no sense to me.  I'll use the dub line to give you a point of reference:

Yuko:  "The entire town is enclosed within a force field.  It's impossible for anyone to come in or to leave.  All communication with the outside is jammed as well."
Rebecca:  "They've switched to backup generators, but all systems are still down."

What the editors did was remove Hitomi into the scene.  Originally, we saw her sitting on top of her Metagross as she spoke.  The new footage on the Japanese DVD makes it so that she isn't in the shot, despite the fact that she still retains the line of dialogue that she has originally.  The result is that it looks like the animators forgot to draw her in that one shot, and this edit really makes me wonder what the DVD authors were thinking.

Visual Edit #16
In the flashback to Deoxys coming out of the meteor, Deoxys is shrouded in shadow again like it was in the beginning of the movie.

Visual Edit #17
Right as Brock says:

Brock:  "Ash!  Look what I just found!  Precious water!"

...there's a shot of Satoshi with a green tint behind him.  The tint, coming from the street lights outside, wasn't there in the original scene.  It seems as if the animators forgot to include the street lights in that one scene, so the DVD authors decided to fix this omission.

Visual Edit #18
As Hitomi studies the various light patterns of the auroras (which leads to the conclusion that Deoxys is looking for its friend), the window border on the DVD version is redrawn to match the window border that we see throughout the rest of the movie.  The icons on the right side of her computer screen are repainted as well.

Visual Edit #19
During this same scene, the windows on Hitomi's computer are rearranged for the Japanese DVD.

Visual Edit #20
Right after Rayquaza passes through the force field (Jenny:  "Rayquaza has broken through!"), the scene is rearranged for the DVD so that Junsa is looking out the same window that she's looking out of throughout the rest of the battle.

Visual Edit #21
This is a weird edit that happens throughout the movie.  I'll just list all of them here.

There are scenes in the movie where characters' mouths are redrawn for some unknown reason.  We never see Rondo-Hakase's teeth bared in this corresponding scene in the DVD version.  Same with Kojirou on the bike or Satoshi among a sea of blocks.  

There may be other edits like this throughout the movie, but honestly, unless I stare at every character's mouth during every line of dialogue, I'm not going to catch them all.  As to the reasons behind these edits?  You've got me.  

Visual Edit #22
The crowd inside the dome-shaped building where the townspeople of LaRousse City are being held has been redrawn on the Japanese DVD version.  The people are more or less the same, but the pokemon shown are different (a Yamikarasu is replaced by some Dewgong, a Pauwau is replaced by some Kyamome, etc.).

Visual Edit #23
During the scuffle between Deoxys and Rayquaza that follows after the second Deoxys is resurrected, a reflection is added to the scene with Rayquaza falling alongside a glassy building on the DVD.  Originally there was no reflection.

Visual Edit #24
During Rondo-Hakase's explanation to his son explaining how to deactivate the security robots, a diagram shows a red arrow pointing to Toh'i.  Originally, that red arrow was a white line.

Visual Edit #25
Right after Toh'i throws his Passport to Satoshi, the block robots rise up and overtake the young boy, Plusle, and Minun.  There are fewer blocks in the Japanese DVD version than there were in the original theatrical release.

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So there you have it.  The question you may have is "Why?  Why were these changes made!?"  There may be a variety of reasons.  Some seem to fix animation errors (Edits #17, 18, and 20) while others may have been made because the director or whoever was in charge of making these edits wanted to make some artistic changes (Edits #03, 08, 14, and 23).  Whatever the reasons are for the individual edits, there is currently no way to own the movie, in Japanese, as seen in Japanese theatres.