In the manga, the opening battle between Rayquaza and Deoxys is just a nightmare that Toh'i has. It's treated like a flashback, meaning that the story of Rekku no Houmonsha Deokishisu, as written in the manga, begins in the present day.

The movie, however, begins four years in the past. After the battle, we skip ahead four years (as indicated by the "Four Years Later" screen in the movie) to the present day. 

Perhaps the biggest difference between the manga and the movie can be found in Rondo-Hakase's lab assistant.  In the movie, she's a caring young woman named Yuuko.  In the manga, he's a backstabbing, glory-hungry man named Haruno.  While Yuuko is a caring assistant who treats Toh'i like her own son and does whatever Rondo-Hakase asks her to do, Haruno wants the crystal core of Deoxys for himself, going so far as to knock Rondo-Hakase unconscious and hiding his body from Satoshi-tachi in order to obtain it.  Haruno eventually turns over a new leaf when the Shadow Deoxys start attacking him, and he exits the manga by simply smiling and walking off by himself.

So why make such a huge change?  Why make Rondo-Hakase's lab assistant the villain of the story?  My guess is that Teshirogi-san was bored with the main Deoxys versus Rayquaza plot, so he decided to add the Haruno subplot to make things more interesting for him.  Personally, I would have liked to see Haruno in the actual movie, since his anime counterpart isn't any different from every other movie's random character of the day, but that's all water under the bridge now.

In the June 2004 installment of the manga, Satoshi and the gang are greeted by an unnamed mechanical dog.  The dog, which welcomes the group to LaRousse City, tries to give everyone a Passport.  However, the dog is mostly ignored, and, after appearing for only two pages, disappears for the rest of the manga.

For a time, many people speculated that the robotic dog was a fourth generation pokemon, much like Gonbe is.  However, no name was given for the little dog, and the CoroCoro Comics magazine never did a feature on the little guy.  Still, there was still a clear division between fans who thought that the Mechanical Dog was a new pokemon and those who thought that it was just another gadget in LaRousse City.

As it turns out, the Mechanical Dog was just a creation of the manga artist, Teshirogi Takashi.  The dog's role is replaced by the infamous Blobo in the actual movie, and since the Blobo play such a significant part in the movie, it's doubtful that Teshirogi Takashi wouldn't have known about their existence.  So why change it?  If I had to guess, it would just be another example of Teshirogi-san wanting to be creative.  I mean, if you think about it, what better way is there to attract attention to your manga then featuring what could be a new pokemon?

Interestingly enough, Teshirogi Takashi later replaced the pictures of the Mechanical Dog in the manga with the Blobo when the manga was collected for the tankouban.  My guess is that the change was done to give the manga more continuity, since it would have been strange to see the Blobo come out of nowhere at the end of the manga had the Mechanical Dog remained.

In the manga, the mischievous pokemon Plusle and Minun steal Satoshi's hat shortly after he arrives in LaRousse City.  In the ensuing chase, Satoshi is lead to the Battle Tower, where he then encounters Toh'i. 

Satoshi arrives at the Battle Tower in a completely different way in the anime.  Satoshi gets himself trapped on one of the automatic sidewalks in LaRousse City and has to be rescued by Ryuu and his Bashamo.  It is then when he meets Ryuu, Shouta, Audrey, Catherine, and Hitomi.  In the manga, he doesn't meet Ryuu and Shouta until his Battle Tower battle with them, and he doesn't meet any of the ladies until after Deoxys begins its attack. 

Gonbe was one of the main attractions of the second Advanced Generation movie.  The never-before-seen fourth generation pokemon was a mystery to most, and fans grasped onto whatever trickle of knowledge was revealed.  We knew that his name was Gonbe, we knew a few basic stats, and we were pretty certain that he was the pre-evolved form of Kabigon.  But other than that, we didn't know anything about what kind of attacks it had or about what kind of personality he had. 

The manga helped shed some light on Gonbe...or so we thought.  In the manga, the gang is attacked by a group of Shadow Deoxys inside the botanical garden.  That much is seen in the film.  However, the way they get out of it is completely different.  In the anime, Ryuu's Bashamo and Satoshi's Pikachu are able to fend the Shadow Clones off long enough for everyone to escape. 

In the manga, however, it's Gonbe who saves everyone from certain doom.  When the gang are being attacked by the Shadow Deoxys for the first time, Gonbe steps up and unleashes a massive yawn/beam attack, completely disintegrating the Shadow Deoxys.  After the smoke clears, Gonbe merely walks away, as if it had done nothing at all.  What's amazing is that Gonbe single-handedly took out over a dozen Shadow Clones, all of which were able to overpower such powerhouses as Bashamo, Kamex, and Metagross.  Suddenly, Gonbe went from being an annoyingly useless comic relief pokemon to being an invaluable part of the plot. 

My only guess as to why this was changed was because Teshirogi Takashi wanted to make Gonbe more special.  He probably guessed that the little guy would be given the title of "yet another useless pre-evo pokemon" (well, he did guess correctly...) so he went and bulked it up a bit. 

The battle between Deoxys and Rayquaza was pumped up to be this epic clash of the titans.  In the manga, the two met over LaRousse City and fought one another nonstop rom the instant the two arrived until a few pages from the end of the comic. 

However, in the anime, the two barely fought at all.  Deoxys had put up a barrier over the city to prevent anyone from getting in or out, and that included Rayquaza as well.  The ozone pokemon wasn't able to break through (and thus, begin to battle Deoxys) until the end of the movie, and even then the two only fought for about five or ten minutes.  So in the manga, we have a huge, Dragon Ball Z-like battle.  In the anime, we have a buildup to the big battle, and then...ten minutes of Hyper Beams going back and forth.  Whoo.

I think it's obvious why the manga artist changed the manga version.

A lot of people have been upset over the fact that the Rocket-Dan's role in the movies has been getting crappier and crappier as more movies get made.  Let's face it--after the second movie, they may as well have not even shown up.  They were mostly used for comic relief, with their only worthwhile contribution being providing background information on the villain (in the case of the last three movies). 

As it turns out, the second AG movie isn't much different.  While Musashi, Kojirou, and Nyasu do get a fair bit of screen time, they still don't really do anything worthwhile.  However, while they are allowed to steal a few scenes here and there (the scene with Musashi rubbing her butt against a robot's face--which will probably be cut out of the dub--is friggin' hilarious) in the anime, they absolutely get the shaft in the manga.  The trio gets a grand total of TWO panels in the entire 143-page manga, and not a single line of dialogue to boot.  In addition, they're shown with a mysterious pokemon (a Koduck, maybe?), giving fans the wrong impression that the Rocket-Dan would have caught the little duck pokemon before the movie premiered.  The movie's come and gone and they still don't have the Koduck, meaning that Teshirogi Takashi gave fans false hope for another (badly needed) Rocket-Dan capture.

Come on...where's the Rocket-Dan love?