Good Idea, but executed poorly
The story, simply, doesn't make sense. While I do credit you for deciding to make a series to help gap the disappearance of Guardia between Trigger and Cross, there are a few things you should note, in both CT Canonology and your own Plotline.
1) Magus, if not killed by the heroes in the game, is revealed to be a "good" character. He's not evil, sure he's dark, but he's not pure evil. Like Hades in Greek Mythology, not evil, simply misunderstood. As Magus is alive in your movie, he shouldn't be that "evil." Also, the heroes are traveling through Time Gates, which were greatly weakened to the extent of not being able to be used at the end of CT.
2) There is no explanation why Magus cared why Taban (Lucca's father) was finding out about time gates, and why he stole the pendant (Which Crono/Marle still owned at the end of CT). Futhermore, there is no explanation why Lucca believed if they recaptured the pendant that Taban could be saved.
Perhaps you plan on answering those questions in your next episode, and stick to the canon a little better to. I liked it, but it was poorly devloped.