Here's how I think FLCL: Progressive and FLCL: Alternative should've been made
FLCL: Progressive – Set several years after FLCL: Classic in which we see Naota getting ready to graduate high school, just when he thinks he has his life figured out here comes Haruko who is still on her crusade to get Atomsk because Naota was the closest she ever came to him.
FLCL: Alternative – This story goes back several years before the events of FLCL: Classic in which we see the story of how Amarao met Haruko for the first time and how she affected him throughout the years.
And that's how I'd handle Progressive and Alternative, thank you for your time