I think they should base future games on MGS3. The focus on survival was great, you could use your surroundings, the story was perfect, the cutscene length was perfect. Some improvements they could make are with CQC, it should be a lot less complicated to interrogate, kill or knock out somebody and stealth should be rewarded more. Bosses need to have a more consistent difficult and need to be more balanced.
If Kojima copied the blueprints for MGS3, added a few mechanics from MGS4 as well as some improvements and new features on top of that, Kojima could have the formula for the perfect game.