Try to break down what you're saying in to basic gameplay changes. The only way it would be interesting is if it were limited, if the resources were finite. But finite resources don't make for a strong ecology. Scarcity is for deserts. We're trying to build a system that allows for an ecosystem, and in a stable ecosystem, it's always a matter of carrying capacity. If the limiting resource is nrg, and only nrg, it makes controlling the pace and flow of an ecosystem much easier.
But we can take the core idea, that bots can do something, and increase the strength and effect of their abilities, and run with it. At present, I'm imagining bots building pretty much every physical object (muscle, other bots, ties, connections, etc.) from protein. Muscle (might/would) be specialized, so a bot could specialize at just shooting, or just moving. Maybe there are some ideas you'd like to explore within this framework. I think there's a post about it in this DB3 forum somewhere.
Nutrients: Essential for lonjevity and Pwaste removal. Implementation in game, Nutrients are heavy and are mostly a sediment based feature, so a bot needs conections or roots to the ground to bring them out. So a bot that feeds from a veg could just gather nrg, but it could also Nutrient steal through the tie. I believe that a veg should have to be fixed when not in pond mode. In pond mode this feature would have to be changed slightly, since it is suspended in the water. This would have a finite number of possible amounts and a finite number of starting amounts, in order to release more decay would need to occur, or a bot would have to consume bots without Nutrients to bio-synthesize this. At no point should the amount of Nutrients in a bot that biosynthesized, intefere with the amount available in the field. A bot can take any other form of body or pwaste and convert it into nutrients with a 3-1 ratio (I.e. 3 nrg to make 1 Nutrient). Nutrient levels should equal pwaste levels to counter the effects of pwaste, but Nutrients cannot exceed the amount of body present by 10%. Why? Because it requires a lot of storage for such a form of energy. At any point a bot can turn Nutrients into energy with a 1-2 ration; 1 Nutrient to 2 energy. This is because biosynthethis uses some energy to make the transfers, so its 100% efficient.
Minerals: Basically a for a pbody; it is not possible to remove heavy elements from the body without an external aid (not presently implemented in game). Minerals should be kept at low levels, why? Simple, if the mineral level should grow beyond the pwaste and nrg, then the Minerals are obsorbing the bots energy and effectively disproving the bots efficiency. How Minerals work for a bot? Minerals are a form of Body, and build up every time a tie feed occurs. It cannot easily be prevented, and leaves the bots body at a logorythmic rate, so the level is never = to 0. It is also recomended that the default settings for Minerals int eh Field be set extremely low. But by having a mineral count between this critical limit and this defaulted 1, a bot can effectively recieve information better and faster through the eyes. I'm not sure if the refvars will eb cycled int eh new DB3, but this would certainly affect any focus switch, it can help to have minerals to function. Minerals help keep musscles moving, joints frictionless and improve thought speeds of a bot. (also not suer if fatigue is going to be introduced). Minerals also allow the biosynthesis of Shells, as well as secondary shot points, they can also repare damage cell walls. 1 Mineral makes 1 Shell.
Vitamins: The building blocks of cellular structurs. Vitamins are the inbetween things; they are stored like fat but with a slight advantage, and can be used as immediate energy with problems in pwaste. Because Vitamins are needed for biosynthesis, no conversions of Nutrients to NRG can occur, or Minerals - to shell. Vitamins also reduce the effective time of venom and poison on a bot. Vitamin levels should not exceed the nrg levels of a bot, but should not be below the level of minerals. For enteractions with minerals, .5 vitamins are spent. Vitamins also allow for obsorbtion of Nutrients, allowing Nutrients to be converted to body or nrg. FOr interactions with Nutrients a loss of .25 is seen in Vitamins. Vitamin level should be considerably low, since it would not take much to see an effect. They can also be biosynthesised inside of veggies, at a cost of 2-1 nrg-vitamins.