First off, In the GS sprite, there are 5 petals(As shown below), but in the Crystal Sprite, There are 6. The question should say "Why was Meganiums 5 petals changed to 6?"but anyway, the only possible reason for GF to change his design, is that they did not like it. They actually changed Meganiums sprite a 2nd time in HGSS, where he only has those weird green lines on 2 of his petals instead of all of them,.
Source: Well most people know the only time they change sprite designs is because they want to improve or make them better. Or they are inappropriate, but Meganium is not so yeah.