Well, I have now watched the complete anime, and Have read the first 6 or so manga. I have enjoyed both immensely, but there are pros and cons to both. (Just as a warning, I watched the anime in English, so any references to voices and so forth refer to the English dub)
The first main difference is that, as is the case in most mangas and animes, the stories are not always in the same order. Personally, I prefer the manga on this. The story-line just seems to flow better, and it leads to less confusion. Also, there are little foot-note like explanations in the manga that define plot, which were lost in the anime, and I really preferred having those to go on.
Personality conflict is handled better in the anime, however. The whole basis of the plot is that Daisuke (and later Satoshi) house an alternate ego in their DNA. However, there are time that Daisuke will be in control, but look like Dark, as well as other, similar situations. When you’re reading, it’s really hard to tell the difference. There were several times I stopped and asked, “Wait, isn’t that Dark? Why is acting like Daisuke?” Then I had to back up and double check the last few pages, to make sure I hadn’t missed one of those tiny footnotes. Meanwhile, in the anime, the voices are markedly different, and makes things far simpler to keep up.
Now, I’m really glad that, for the most part, the anime and manga are of similar quality, and they are both very good. I personally preferred the manga, mostly on the basis that the girls screaming in the anime got on my nerves. However, whether you prefer to read or watch, this is a series I certainly recommend.
Happy reading/watching! (DragonRider)