Despite directing the 3D demo, Kojima may not be in charge of the final game.
http://www.nintendoworldreport.com/news/23627
In a feature in this week’s Famitsu, Metal Gear Solid creator Hideo Kojima talked about his involvement with the Metal Gear Solid 3DS demo shown at E3. The development of this tech demo started after Peace Walker was completed. Kojima reunited his team and told them that they would be making a demo for E3. The development of the 3DS demo was kept secret, with the team placed on another floor, making people believe that the team was on vacation, according to Kojima.
The demo was based on of Metal Gear Solid 3: Snake Eater for the PlayStation 2, but some of the character models and backgrounds were redone. "The high level models are about the same quality as the stuff we made on the PlayStation 3, although it's tough to see this. If we'd had a bit more time, we could have made something better." said Kojima to Famitsu.
When asked if Kojima would direct the final 3DS game he said that, "I was the director of the demo. What will happen from here on out is not set." The interview notes that the game just started development. To this Kojima adds that, "What we wanted to do this time is show that we're making an entry in the Metal Gear Solid franchise that can be enjoyed in goggle-free 3D on the 3DS." With the possibility of the final game being a remake of Metal Gear Solid 3, Kojima explained that "MGS3's story can't change, so we're thinking of Co-ops, 3D and portable-like elements."