It may be fair to say that all Metal Gears up to and including MGS2 had similar design agendas. They were attempts to model, at increasingly levels of complexity, the core concepts of military espionage. Basic things like sneaking around, taking down enemies silently, and what to do when they found you were the main things being experimented with and revised. This all changes with MGS3.
Metal Gear Solid 3: Snake Eater (PS2 2004) on the surface seems much like MGS2. It has the same basic controls, the same mechanics of sneaking, of holding enemies at gunpoint. It has the same enemy alert phases from MG2, with their expanded enemy behavior from MGS2. It has the choking from MGS1, and (in a fashion) the same radar system. MGS3 reshuffled these familiar elements, however, giving them new meaning in a different context. A lot of it grew out of a decision to partially remove the radar, by breaking it up into two separate radars that (thanks to finite battery life) could not be used indefinitely. The radar first introduced in MG2 and revised in MGS1 showed enemy position, movement, and terrain with 100% accuracy. The radars in MGS3 showed neither terrain nor enemy vision. One showed moving life forms; the other stationary life forms. And since screens in MGS3 (thanks to its wilderness setting) were filled with animals as well as enemy soldiers, using these radars became a game of detective work, one that required cross-referencing with the player's knowledge of the current terrain and its wildlife. If the difference between soldiers and animals could not be determined, the player's directional mic (which could hear footsteps) was often the only way to definitively tell. The directional mic was introduced in MGS2, where it had limited, special-case application. In MGS3 it became part of the player's core gameplay vocabulary. Unlike MGS2 the player began the game with the directional mic, which made listening a new core action at the player's disposal. By limiting the player's ability to see, but enhancing their ability to hear, MGS3 made the process of simply finding enemies a major aspect of play.
Fighting an invisible enemy--of finding them before they found you--became the defining tension of play, which gave the expanded enemy interrogation mechanics a whole new value. Interrogation went from a cheap way to get items (in MGS2) to the primary mode of gaining gameplay-related information in MGS3. The choke action from MGS1 was retooled to be non-lethal: now a grabbed enemy could be squeezed for info. A chatty enemy could give away the positions of his comrades, which showed up on a sub-screen map. This effectively recreated the same radar information enjoyed in past games, though only after significant thought and planning. Discovering enemy positions in order to avoid (or subdue) them was much more important in MGS3 because the alert phases were much, much longer. Enemies would now search for a matter of minutes, not seconds. Even if the player escaped with their life, they were punished by having to wait for an agonizingly long time for enemy units to perform their sweep-and-clear patterns. Impatience could result in endless chases and gunfights over a wide variety of terrain. And although the player could sometimes call off an alert using the enemy's radio frequency (another useful bit of info that could be procured through interrogation) the only surefire way to achieve your objectives was patiently shaking down soldiers for field info, until you were 100% certain your imaginary map of the situation matched reality.
Interacting with these re-tooled old systems were MGS3's new systems, namely its camouflage and stamina systems. The camo system allowed the player to change Snake's outfit at any time, into a variety of patterns and colors. The closer the pattern and color was to the texture Snake was currently on (grass, gravel, tree bark, mud, sand, etc.) the higher the "camo index". An index of 0 was total visibility. An index of 100 was total invisibility. What was interesting about this system is how it reconfigured the entire game map in an instant based on the player's chosen camo. Similar to Ikaruga, which involved as its principle player action the inversion of hot (dangerous) and cold (safe) space, MGS3 offered players the strategic affordance of deciding for themselves what spaces would be hot or cold. A tree trunk was as perfect hiding place in tree bark camo; a horrible one in snow camo. In past Metal Gear games the configurations of hot and cold space were always fixed, and this fluidity made MGS3 a different strategic animal than other games. It wasn't about finding safe spots so much as creating them, something which was only made possible by its organic (and often vast) wilderness environments. Although there were a few indoor locations that required the symmetrical, ordered thinking of past games, most spaces in MGS3 were messy and sprawling. Some screens contained acres of chaotic, tangled undergrowth, where textures and colors mixed and swirled together in crazy ways. Learning to read and exploit the potential of the natural world was really the main challenge of MGS3. Both you and your enemies were at its mercy, rendered obscure by its twisty madness. Using nature better than your foe (who were also somewhat camouflaged but, unlike you, couldn't change their camouflage) was the order of the day, and it meant the difference between success and failure.
The theme of wilderness survival reached much farther than just manipulating visibility (and therefore combat advantage). It was also woven into the mechanics of health, which departed sharply from past Metal Gear games. Health was no longer replenished by healing items. The player had to wait for their health to recover naturally over time, which was essentially an expansion of the bleeding-recovery mechanic from MGS2. Like bleeding had previously, overall health in MGS3 would recover faster if the player lied still. Lack of stamina would also impede health recovery, as well as cause a host of other ill conditions. Like the directional mic, MGS3's stamina meter was a core game system generalized from a past game's special-case function. It was essentially a re-tooling of the grip meter from MGS2, which governed how long a player could hold onto a ledge. Unlike the grip meter, the stamina meter was on-screen at all times, and would deplete for a variety of reasons. Running, swimming, fighting, hanging, or just natural hunger: all these things would make stamina deplete. Low stamina caused not only slower health regeneration but also diminished aiming ability. The screen would shudder while in first-person mode, making it harder for the player to perform effectively in battle. All this necessitated catching and eating the live animals littered throughout MGS3's wild world. Only by eating the right animals (and avoiding the wrong ones) could the player maintain their health and their physical combat performance.
Far from being just a localized mechanic, eating and stamina in MGS3 was a global system that governed all human behavior, not just Snake's. All enemies had stamina, which depended on stores of food rations scattered throughout the wilderness. Sneaking into and blowing up one of these store houses would cause all enemies in the nearby area to starve, giving them all the same low-stamina effects you would suffer under similar conditions. Their aim became worse, and a single punch would cause them to fall unconscious. Destroying the enemy's non-food resources was another way to manipulate their behavior. Blowing ammo stores made them less likely to waste bullets unless they had a clear shot. This, combined with the fact that enemy soldiers would not shoot a comrade you were holding, gave shrewd players enormous leverage should they find themselves cornered by an group of numerous--but tired and under-equipped--enemies. Taking a hostage, backing towards an exit, and then making a break for it as the few bullets your opponents had missed you by a mile was just one way to bend these logics to your ever improvisational advantage.
Metal Gear Solid 3 is a great example of existing game mechanics reconfigured to create a different game from its predecessors. With the core mechanics of military espionage more or less solidified after MGS2, MGS3 feels like a conscious experiment to explore new flavors of (rather than just better or more complicated) stealth gameplay. It does this by focusing on a setting and a theme, and allowing that setting and theme to both inspire new mechanics and reshape existing mechanics. As a result MGS3 is a game about wilderness survival as much as it is a game about sneaking behind enemy lines, a fact that can be felt coherently in every aspect of its design. This man versus nature conflict, embodied globally in the game system, might explain why enemy soldiers seem a bit more human than before, for now they are unambiguously subject to the same forces as the player. In many games the rules that govern non-player characters and those that govern player-characters are different, but in this game they are the same. Understanding this, that your foe contains all the same human frailties you do, is your key to to defeating him in MGS3's unforgiving world. As we'll see, this gradual humanization of the enemy will only increase as the series progresses.