The way I'd like to see an open world Metal Gear work would be to create environments that live on their own and give you a number of objectives to complete in that environment. For example you might have an airbase where you need to sabotage a plane, steal some flight plan info, and take pictures of the cargo. It doesn't matter what order you do that in and the enemies on the base could change their actions depending on how you completed the objectives. In that environment NPCs wouldn't just be on the standard MGS patrol routes. Some might be, others might be doing chores, or relaxing. I'd love to see NPCs react differently to the signs they find that you're there. Taking out security cameras might results in extra guard patrols, finding a dead body might cause one reaction, finding a bunch of dead bodies might cause a completely different reaction.
I'd like to see smaller open world environments that have all the detail that typically goes into an MGS level. It also still sets up a very story driven game rather than a game where you goof around and get to "story" missions whenever. Love it or hate it, MGS needs the crazy story, characters, and even the silly game mechanics for it to be a MGS game.