Not sure as to why, but i'm sure he'll still be involved in the musical world in way one or another.
You're right, it has been in the works for a while.
he's constantly been distancing himself from rumours of a new album and apparently in a radio interview a month ago he asked to be introduced as "guitarist, John Frusciante" not "Red Hot Chili Peppers guitarist, John Frusciante".
He's definitely his own man and i'm guessing he just felt the time was right or that the new album was going nowhere.
Josh Klingoffer (John's best mate and RHCP tour guitarist) is rumoured to be the replacement.
Either way, John is my musical idol so i'm a very shattered man right now!