Well the anime and manga were slated to end about the same time, however it's likely a combination of delays and the simple fact that Daisuke didn't have direct work with the anime that lead to it overtaking its source, thus a new ending had to be cut from whole cloth.
Though the manga had better characterization, artwork, and flow, some of the reveals became flat out weird. Like demons actually being aliens, the whole thing went from supernatural to more sci-fi.
But when you get down to it, none of that really mattered. What mattered was Chrono and Rosette.