How exactly does one get all of the skills in 30 hours?

Well, I can see how if you skip a lot of the movies.

Regardless, in Xenosaga 3 each path each character can take is unique.

It's not like you can run Ziggy down one of Shions paths. The two paths for him are unique to him and him alone. Even if you get both done, your characters are still all very unique.