When someone refers to Pokemon "manga" generally they are referring to the Pokemon Adventures Manga. Generally speaking, pokemon has suffered from a lack of a truely strong and widely published manga. There have been a few comic books though those were published back when pokemon first got started, but the comic books were mostly short series, perhaps 10 comic books at the most. When I speak of "manga" I'm referring to the fact that Pokemon has never had anything that was as popular as say Naruto, Bleach, One Piece, etc. With Naruto at over 400 chapters as of this writing and Bleach approaching that number as well, with scannalation groups devoted to translating and releasing weekly publications of naruto and bleach manga, I think it's clear that Pokemon does not possess anything of that caliber. Why is that?
I figure a large part of this is due to the demographics of Pokemon communities versus OnePiece, Naruto, and Bleach communities. After all, Pokemon began as a video game and then anime and manga adaptations were taken from there. The other manga began AS manga and were adapted into a tv show and into spin off games. Perhaps it is because the anime has generally performed very poorly in the eyes of the online pokemon community that the manga was not given a proper chance. Of course some of the blame lies with Viz as well, since Viz did a very poor job of circulating the Pokemon Adventures manga and getting it out to the public. Other reasons could be that due to the lack of a scanalation group in the pokemon community has prevented even an online buzz over the manga being generated, whereas the games are clearly widely publicized and hailed throughout the pokemon community. Another possibility is that Nintendo itself has never been a strong influence on manga or comic book adaptations of it's various franchises, whereas OnePiece, Bleach, and Naruto were pushed by their authors. Nintendo does seem to demonstrate some monopolistic tendencies towards its franchises. After all, Wizards of the Coast lost the rights to the trading card game in 2003, and more recently 4Kids lost the rights to the anime. Not to mention that Nintendo does hit hard on copyright violations as well, all of this may also contribute to a reluctance on the part of the pokemon community to actively involve themselves in distributing scans of the pokemon manga.
Regardless of why Pokemon Adventures isn't very popular, and the same can be said for several other different pokemon mangas; others do actually exist and are even less well known, the manga is excellent. Of course it's excellence could be due to the fact that it looks so much better when compared with the anime. At the same time though, it does at least favorably well when compared with Naruto and Bleach, as far as the quality of the storyline goes.