I do not own the Metal Gear franchise, all rights to the series go to Hideo Kojima.
In the comments, suggest something to add, but please note this one detail. I am NOT adding any Metal Gears. Now, have fun!
I can see a lot of potencial in this mod. Woud be amazing to see the Metal Gear series in Minecraft, but I do think you could add the following features into the mod. I'll put the suggestions into a spoiler for you, as it may take up an entire page.
Weapon Extras e.g. Suppressors and Laser Pointers
Allies e.g. Otacon, Raiden, Meryl and Roy Campbell
Villains e.g. Revolver Ocelot, Liquid Snake, Psycho Mantis and The End
Vehicles e.g. Jeeps, Boats and Helicopters
Metal Gear Battle Tanks (I known you said you wouldn't add them, but what's a Metal Gear Solid mod without these beauties)
A Stealth System/Enemy AI
Bases and Enemy Outposts
I won't bore you with other suggestions I have, so I'll leave you with these.