By that, I mean what are the advantages of a Bipedal, Silo-less nuclear tank.
The Metal Gear wiki states that it's purpose is to "destabilize the global balance of power via the threat of covert long-range nuclear attack" and to "connect infantry with artillery, making it invulnerable to firepower shortages and terrain"
The problem is that mobile, bipedal tanks aren't covert at all, are vulnerable to artillery, and are designed to launch nukes, which doesn't address ammunition shortages.
Best Answer
Metal Gear would absolutley destroy the foundation of war as we know it. It's, as stated, a Bipedal nuclear weapons system. This would create all kinds of issues as it would give it's controller the ability to launch a nuclear weapons attack from anywhere on the world. In addition, it's mobility completly takes the 'range of the missile' out of the equation as it could just walk within range after being dropped off where-ever it needs to be.
While nuclear subs have this ability to some extent, Metal Gear takes it beyond just a step further. Subs are much easier to find. Metal Gear is, indeed, covert, as it is so small, in addition to it's other attributes, that it could be easily hidden from enemy detection until needed. IE: in an underground bunker. Most detection methods are designed to find an object that is either much larger, or (speculation here) designed to give off a much stronger heat signature.
The "connect infantry with artillery, making it invulnerable to firepower shortages and terrain" part of your question I daresay is the easiest to answer. It's a mechanized battlesuit my man. The very DEFINITION of next-gen warefare. Militaries all over the world (in real life) have been trying to create this very thing, or something similar to it at least, for years. Do you have any idea how much ammo weighs? Or how much more that weight feels like after youve patrolled on foot for twenty clicks? Or how much for that matter your ARMOR's weight feels like and is? (anti ballistic vests and such)? -- And terrain is a JOKE. It dictates everything about everything we do as soldiers. We are not hindered so much by our equipment, physical fitness is the counter to that, or by our enemy, superior tactics and know-how counter that, but terrain is un-conquerable. It either allows or denies a mission with absolute authority. Climb a few clicks up a mountain because it's in your way and then tell me different. Metal Gear (or just about any mechanized battlesuit for that matter) COMPLETLY eliminates any kind of hindrance from everything I just covered here. Sure its ammo is feasibly exhaustible, but when you have a hard time carrying 60-80 extra pounds of rounds, having SEVERAL TONS OF IT at your disposale changes the game in a whole new way.
Afterthought: I have since learned that my idea of how subs work was sadly mistaken, but the basic premise of my answer remains sound. I'm going to leave the answer as is.