It appears that Hideo Kojima will be stepping down for the next Metal Gear game to take a hands off 'creative director' role. Production duties will instead be passed to MGS3's Executive Producer, Motoyuki Yoshioka. It's believed that MGS3 was his trial run and judging by the quality of MGS3 which he co-produced with Kojima, he was, without doubt a resounding success.
This news isn't particularly new, as back in November 2004 senior Konami executives revealed the existence of MGS4 during a financial conference call, stating that work had already begun. This indicates that Konami must have been in possession of rough PS3 specs as early as mid 2004.
MGS4 is likely to take the series in a new direction. Kojima has said that MGS3 will be the last in the trilogy. It is not known which timeline or locations the game will feature. It could be set in the 1960’s Jungle like MGS3, or perhaps Metal Gear Acids fictitious Tejan Republic of South Africa in 2016, but most probably the game will factor in some new location/timeline and even main character.