2 Other factors also come to find.
1. Kojima recently tweeted that 1 years worth of work was just shut down the drain. No one really know what that meant but it's possible it relates to the differences we're seeing in the game here.
2. Konami recently announced the HD collection for MGS. Was some of the team responsible for the 3DS MGS3 moved over to the HD collection and/or is it possible they wanted the HD collection to look as best as possible against the 3DS version to increase sales on the platform better known for MGS games?
Kojima tweeted that the remaster games were being handled by the studio (Bluepoint Games) that did the God of War I & II and ico game remasters on PS3 so that development shouldn't affect the 3DS game at all, which is probably being handled by a seperate studio where as the E3 tech demo was probably handled internally.