Is there going to be a flcl season 2?

Yes, there is a second season of FLCL, called FLCL Progressive! It was released in 2018 and is a sequel to the original FLCL.

There's also a third season called FLCL Alternative, which was released in 2019 and acts as a sequel to FLCL Progressive.

So, while you might have been wondering if there would ever be more FLCL, it's already here!