The only thing I didn't like about the manga handling of it was that they made Archie and Maxie seem like completely evil monsters instead of just simply misguided villains like they were in the games. I guess they didn't want the R/S arc to seem like the Yellow arc with the same type of villain, i.e. a misguided person who thought they could make the world a better place by causing death and destruction using Pokemon. I guess I can understand that reasoning, though that resulted in Archie and Maxie getting no closure in the manga. Oh well, it still beats the anime by a mile, because it involved people who were *supposed* to be involved like, say, Steven and Wallace. Together. Fighting side by side. <3
One thing both the anime AND PokeSpecial manga failed to do was emphasize Wallace's importance as the Guardian of the Cave of Origin (and, in Emerald, the person who had the key to the Sky Pillar--they gave the Sky Pillar job to Norman in Special...I guess because he was the hero's father). The manga only made one mention of Wallace's status as Guardian of the Cave of Origin, somewhere in volume 18, then never expanded on it.
But still, if the anime had been anything like the manga in their treatment of the Kyogre vs. Groudon battle, I'd have been much happier.
Incidentally, is anyone else annoyed by the fact that Diaruga and Parukia--who are never mentioned in Diamond or Pearl as having fought each other--get a WHOLE MOVIE where they fight with each other, while Kyogre and Groudon--who even in Ruby/Sapphire were mentioned as having fought in the past--get those two crappy rushed episodes?