While there was enough Foreshadowing to justify Gooyan being The Man Behind the Man, the fact that he created Akudaikahn doesn't seem to make much sense.
Still, Goyan is shown to be much disliked by his allies. Perhaps Akudaikahn was supposed to be a puppet king. Soldiers of evil would be more willing to follow a giant menacing monster than an annoying and short green guy.
In anotehr dub of episode 1 when Saki tells her father to change car, instead of saying that 'everything has a life inside it' like in the original, she says that 'everything has an end'. Truly fitting words to symbolize the end of an era and the start of another.
The sea being the Fountain of Sun makes sense when you consider Earth lifeforms evolved from aquatic creatures. As it said that the Fountain is from where all spirits (essence of living creatures) came from, what kind of body of water that qualifies that condition other than the sea?
Goyan's absence after being defeated by the Pretty Cures the first time was because he needed to persuade Kintolesky to confront the girls. He perfectly knew that showing up before Akudaikahn after having failed would have been a terrible idea so he decided to take his time to return with something in his hands other than a failure.
