Decay is a natural part of life. All things that live on Earth must also die at some point. And on one's journey through life a person experiences much decay. From one's mental/physical health to the accuracy of one's memories every tangible, quantifiable part of our being decays with time. And it's not just living creatures. Houses even grow old and crumble. The unrelenting wear and tear of nature can weaken and topple buildings never mind the storms that can rock entire cities at a time. Even the very atoms and particles in radioactive materials are known to just up and leave predictably.
We're all trapped on this planet in our respective biomes, and so is the decay. Fortunately everything we don't jettison out into space eventually gets recycled back into the realm of the living. Material is consumed, broken down, entered back into the cycle and consumed again. It may sound less than appetizing but this is a reality we've all gotten quite used to by now.
So if you think about it, in the quest to follow what is perhaps the most important tenet of Classical Game Design "form fits function," when using natural, organic forms designing some kind of decay system appropriate for the forms is only natural. If you're going to give the main character the ability to throw stones, then it only makes sense that the stones come from a limited supply as well as remain on the field for collecting. Such was the case for Neo*RPG.
As I have said before, my understanding of Classical Game Design wasn't nearly as clear in my head or articulated on paper when I developed Neo*RPG. Guided by instinct, I simply tweaked every facet of Neo*RPG's design one step at a time until I was satisfied. In this case, reducing the clutter and abstractions from the game was satisfying.
So, I started with a simple rock throwing mechanic. I had intially given the player infinite rock ammunition. Furthermore, after throwing a rock the projectile disappeared. After play testing the game and thinking about this particular mechanic, I developed the same kinds of thoughts that I imagine anyone would formulate. Where does the character get all of his rocks from, and when do they go after he throws them?
To fix this issue, I gave the player a limited number of rocks to throw in addition to programming the rocks so that they remain on the ground after colliding with an object or coming to a stop. After this adjustment, it naturally followed to give the player the ability to pick up rocks from the ground to add to their ammo supply.
From this point, it was easy to design the archer enemy that obeys the same rules of decay as the main character. Both have limited ammunition, and both must move through the environement to collect rocks to resupply themselves. In this way, the rock throwing mechanic is organically designed to decay and renew itself in a closed cycle.
Organic decay-cycles are difficult to come by. Most developers rely on some kind of spawning system to resupply the player whether its randomly dropped powerups from defeated enemies (Megaman, Metroid), supplies hidden in regenrating pots (Zelda), or merchant/shop transactions (RE4, RPGs). In all of these cases, the supplies are generated by the game in a cycle that is disconnected from the organic forms of the game.
Fortunately, some first-person shooters have ditched randomly scattered ammo crates forcing players to take enemy rounds to maintain supplies. After all, if the enemy is using the same gun you are, it only makes sense to be able to use their unused ammo. Halo does this very well. In Halo, players can only carry 2 weapons at a time. When the ammo runs out in one, players commonly swap the empy weapon out for another gun they find lying around in the field. The number of rounds in the new weapon is exactly the same amount that was left from previous use. This design may create some frustrating moments when you fight for a power weapon that in the end only has one more shot left, but the transfer of weapons and ammo orgnically from one player to the other not only creates an organic decay-cycle, but the design creates interplay as well.
Designing decay into a game system must be carefully balanced. Every form and mechanic doens't need to decay in a game. Finding the balance between which elements to add decay is a matter of how the designer wants to shape the depth, expression, and definition of the game's primary function. If the function of a game is to battle, then it makes sense to design decaying ammo and attacks. If the function is to live a life and communicate with others, then it probably isn't a good idea to have my furniture in Animal Crossing fall apart over time. Calling a repair man, and negotiating insurance polocies on my possessions would probably be a diversion from what Animal Crossing is all about. In other words, all games aren't trying to be simulations.
And this isn't even considering the fiction or conceit of a game. In Ikaruga, the main character flies a special air craft in an aerial war of some sort. This air craft has the ability to ABSORB (the primary mechanic) and SHOOT an infinite supply of polarized bullets. Everything in this game (minus the white birds at the end) reflect some kind of futuristic technology. It fits well within the fiction world that an air craft can shoot and absorb an endless assault of bullets. Adding decay to either of these mechanics is simply a matter of preference.
At the end of the day, a game must work. Every element of a game can't be completely organic following form fits function and incorporating a complete decay system. If that were the case, we'd be flooded in simulation games. Even the stale-move negation in Super Smash Brothers Brawl, for the most part, only weakens moves that do damage to an enemy. So, all those attacks that don't connect are still at an undecayed level of strength. The general concept of moves weakening with repeated use is still intact, but it's carefully balanced to encourage play where players are free to attack as they please and hope for hits instead of worrying about weakening their characters.