The manga might use visual cues to imply certain things. For instance, the expressions of the characters can convey a lot without the need for too many words. The novel, being a text - based medium, has to describe these things explicitly. It will use detailed prose to describe the settings, like the strange and dreamy worlds in Kingdom Hearts, which might give a different kind of immersive experience compared to the manga.
It depends on your preference. If you are a visual person, the manga might be better. The art in the manga can quickly show you what's going on and the character designs can be really appealing. For example, seeing Roxas' journey through the beautifully drawn panels can be very captivating.