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A Look At the Tools Used To Make Metal Gear Solid 4
Soft Image is running a detailed story about the making of Metal Gear Solid 4. They explain the game's development cycle, from the art direction to the animation of characters to the building of models and textures.
"In terms of bones used for constructing the bodies of characters, about 21 joint bones were used that contained animation data and were activated through these data. But many auxiliary bones were also used to supplement movements such as the twisting of knees, elbows, legs and arms. These were not activated by animation data. Rather, they were linked to the values of the basic joints that were activated by animation. ... They also used a tool to automatically generate the rig for controlling eyeball movement and the muscles around the eyes. Because the area around the eyes is also controlled using both shapes and bones, when the eyeball locator is moved, the muscles move smoothly just like they do for the mouth. Further, even if the shape is edited to redefine the eye edges, it does not spoil the blinking or brow furrow expressions at all."
Softimage [sic] is a company that makes 3D modeling and animation software. As such, their part of the story isn't related to gameplay at all, which is why only art and related programming was mentioned.
The original (2D) game was just called "Metal Gear". You played as "Solid Snake", and were trying to destoroy the ultimate weapon "Metal Gear". That made sense to me, even if the name Solid Snake seemed unfitting for a high-tech soldier.
I've always taken the "solid" moniker in the name to mean that the game had moved to 3D, and now had a solid environment instead of a flat one. After all, the second one is not called "Metal Gear Raiden" or anything.
Of course none of this answers your question. I've wondered myself, to be honest ;-)