1. The Boss
The Boss is one of the most important characters within the franchise and it would be awesome to have a game set in World War Two where you play as her and can witness the creation of the Cobra Unit.
2. Gray Fox/Frank Jaeger
Remember how awesome it was to play as Gray Fox in the special missions? A game showing how he went from being normal to being given an exoskeleton would be great and it would cool to play as him during his infiltration of Shadow Moses.
3. Remake of the original/second game
I, like many others, have never played the originals and whilst I will when the HD collection comes out I'm sure that, although I will probably enjoy them, I'd crave a complete remake of them.
4. A game as Raiden in his child soldier days
Kojima probably wouldn't be allowed to make a game about a child solider but I'd love to know about Raiden's origins especially as I seem to be part of a minority that actually quite likes him (if you think about what he did in the second game he is quite a bad ass.)
5. Liquid's days in the SAS
Liquid is my favourite villain ever and I would absolutely love to know more about him and to finally be able to play as him but not within the realm of an existing game. It would be a great fan service and a great way of fleshing out Metal Gear's awesome story.