Joss Whedon (Serenity, Buffy The Vampire Slayer, Angel) has now gone on record saying that he will NOT be involved with X-MEN 3. "....I wasn't asked to write and direct X3", the director says.
Recently, executive producer Avi Arad mentioned that Whedon was in the running, which has caused some confusion. XMF thinks that while Whedon was indeed being looked at as a possible X3 canidate, he was NOT in considerations to both write and direct the film project (something Whedon does on all of his projects).
So who are the other possibilities for X3 director? Early rumors suggested Alex Proyas (I, Robot), but they were just that....rumors. Proyas has gone on record saying that he wouldn't direct any film in a franchise he didn't start. Major contenders for the job could be: Doug Liman (Mr. and Mrs. Smith, The Bourne Identity) and Rob Bowman (Elektra, The X-Files). Both directors are currently finishing work on blockbuster films for the studio, and have had great past experience directing ensemble casts.