For story it would be MGS3 Snake Eater, for Game design and engine it would be MGS5. MGS5 is the perfect metal gear, although the story elements are lacking in some respects especially how it 'recycles' mission. I thought it was really bad. But this was definitely what a perfect MGS Kojima was aiming for in terms of game design (and not the story). If they do a remake of MGS3 using MGS5 engine and mechanics it would be awesome.