In an announcement from Toonami last week, they announced that they are making FLCL seasons 2 and 3!!!
They're gonna do it with Production I.G. according to the statement.
Check that out:
Toonami is proud to announce an original co-prodution with legendary studio, Production I.G, “FLCL” seasons 2 and 3! That’s right, we are producing 12 new FLCL episodes to be split into two seasons, and serve as a sequel to the original classic, FLCL! Stay tuned for more info when we have it!
The press release from Turner Broadcasting says even more:
"In the new season of FLCL, many years have passed since Naota and Haruhara Haruko shared their adventure together. Meanwhile, the war between the two entities known as Medical Mechanica and Fraternity rages across the galaxy. Enter Hidomi, a young teenaged girl who believes there is nothing amazing to expect from her average life, until one day when a new teacher named Haruko arrives at her school. Soon enough, Medical Mechanica is attacking her town and Hidomi discovers a secret within her that could save everyone, a secret that only Haruko can unlock.