So my game takes place in a robotic universe where every living things is a machine.

The problem is that I am conflicted on how I want plants to work, and how bees should work. Every living thing in this world need fuel and metal.

The first way is to mimic the pollinating. Bees land on plants to harvest liquid fuel (same as real bees and nectar), the bees also collect nano bots for metal (pollen collection). Once the bee lands on a other flower some of the nano bots dislodge from the bee and enters the new plan't ecosystem, once inside they transfer data from the original plant to the new one; this results in seeds and new plants.

This way plant seeds have to be collected for farming and bees are most useful to the players as a source of fuel. If I decide to add effect weapons like ice grenades, players will craft them from plants or maybe use the plant seeds as grenades.

The thing I like most about this is it feels natural, it could even make players more aware of how our own ecosystem works.

The second way is data transfer. have bees land for fuel and nano bots, however the plant injects it's data into the bee, either wireless or with a USB. The bee then acts as a living seed, it can fly around with a timer and once it reaches zero the bee plants it's self into the ground.

This way the bees can also be used to plant flowers, like the butterflies in Don't starve. The bees could also then be said to contain the materials of each plants an can be used as grenades.

What I like about this is no crafting is needed, the bee is more useful and important to the player(it's taking some time to model).

I prefer idea #1 because the idea of a bee burrowing itself into the ground bugs me for some reason. I guess my real answer would depend on what sort-of game you're making in general. Farming simulator? Survival? Something completely different?

What sorts of fuel and metal are used?

I don't see the benefit to the "bee" in the second scenario. I mean, there could be some malicious plants that infect bees to turn them into living seeds, but if the entire ecosystem is built on that, you're going to run out of bees.

Also note that in a robot world, your larger plants won't necessarily need intermediaries to transmit data; a big, powered metal stalk can be a radio transmitter/antenna on its own, with a reach of the square root of its height times about 3600.

Except, you know, rocket-propelled seeds.

This is a good point, didn't think of it like that. This could make for some interesting results. It also matches the first pollinating type. It could also result in a lot more animations that is easy to achieve, allowing me to create more of a artificial living world.

I prefer idea #1 because the idea of a bee burrowing itself into the ground bugs me for some reason. I guess my real answer would depend on what sort-of game you're making in general. Farming simulator? Survival? Something completely different? What sorts of fuel and metal are used?

The game is a group survival game, with the player building a colony of AI, to survive and retake there home world.Building and resource management is a very minor goal in this game, that is why only two resources exist.

Exploring the world is what I want players to focus on.

Metal is used for building, creating weapons and tools. There are no other resources for this, instead the amount needed for building is huge.

Animals eat metal to regain health, once they have reached a amount of metal requirement, they can also upgrade to a stronger version.

Fuel is used for power, the player and animals needs fuel to keep there battery charged, what kind of fuel can be converted to energy depends on what upgrades are equipped; most animals stick to one kind of fuel. Fuel is used by the player's home to actively run any automated machines.

Animals with no fuel can have a small solar panel that allows them limited functions, however if a animal reaches zero fuel and has remains deactivated for long, it will be broken apart by nano bots.

The reason I thought of the bee idea was because it was alien and allowed player manual control, although with seeds and plants it's still possible. Also at a more advance stage the player can make planter and harvester bots.

Why do we have to be binary? Some of the best ideas are the merger of two previously best ideas.

Merging all of the elements will be to much, the personal goal for me with the game is to keep everything as simple as can be.

It should be nothing but the bare bones of a survival game.

I don't see the benefit to the "bee" in the second scenario. I mean, there could be some malicious plants that infect bees to turn them into living seeds, but if the entire ecosystem is built on that, you're going to run out of bees.

Maybe only having some plants act like this is a good idea, it will allow me to keep both ways and even give players more content to see.