If we wish to introduce different gameplay patterns across different metabolism forms, here are some ways we can achieve this, as well as a proposal for how each different metabolic pathway can be thought of.
Metabolism Benefits and Risks
Oxygenic - High Risk, High Reward
Oxygen will serve as the quintessential high risk, high reward metabolism in the Microbe Stage. The oxygenation of a planet comes with intense challenges and benefits for the life inhabiting it - adapting to use oxygen allows access to the most powerful metabolic process known, but its toxicity and availability makes that adaptation process a challenge to undertake.
Since oxygen will likely be the most necessary compound for progression beyond the Microbe Stage, the challenge related to oxygen should probably be represented mostly in the Microbe Stage, and should mostly be related to the acquiring of oxygen. We will likely have to ensure that oxygen can’t dip too much beyond a certain threshold once reached.
Risks
- Oxygen is initially a very unstable resource.
- Oxygen is initially toxic to organisms.
- Requires a stable source of glucose, either prey or ambient.
Rewards
- Most energetic and powerful metabolism available.
- Important for progression beyond the Microbe Stage.
Photoautotrophic - The Tight Schedule
In applicable regions, photosynthesis will generally be defined by the day and night cycle; a consistent, but demanding schedule requiring behavioral or morphological adjustments.
Since photosynthesis’s inherent advantage is its predictability, disruptions to this schedule - such as volcanic events or snowball Earth - represent the most challenging moments for photoautotrophs. Though consistent, players will have to be mindful of the fact that if they do not efficiently adapt to photosynthesis or have a reliable alternative metabolic strategy, disaster can strike.
Risks
- Day and night cycle requires concessions.
- Not very energetic.
- Limited to surface patches and light as a whole.
- Adaptations should make it harder to be actively heterotrophic.
- Produces oxygen.
- Chloroplasts and thylakoids are very heavy
Rewards
- Very stable and predictable energy source.
- Autotrophic, self-reliant.
Sulfur - Managed Risk
I will note that hydrogen sulfide/sulfur might be subject to change if we cannot find a good way to implement anaerobic respiration with currently integrated parts.
As @Titan mentioned, hydrogen sulfide can be toxic above a certain capacity, and can be more toxic for organisms who do not ingest hydrogen sulfide. Based on the number of chemosynthesizing proteins placed, the capacity for hydrogen sulfide tolerance can increase. This will incentivize players who utilize chemosynthesizing proteins to specialize more around them, or avoid them.
This can benefit Thrive in other ways as well. Hydrogen sulfide can serve as a proxy for the fumes which make hydrothermal vents and volcanic activity potent for unadapted organisms, thus including an environmental hazard in these more harsh conditions.
Risks
- Ingesting too much sulfur will harm the player.
- Sulfur is more limited to deeper patches.
Rewards
- Provides some security, as not all organisms can inhabit sulfur clouds.
- Can provide a relatively accessible food source.
- Mitigates environmental harm.
Iron - Territory Wars
Currently, Iron is a more unique diet since it requires some sort of harvesting. I think this can be improved by limiting the amount of iron available to be consumed from chunks and large emitters more strictly, rather than have them passively and consistently emit compounds. This can enhance competition for chunks and parts, forcing the player to be more territorial over their discovered parts.
This would likely require a rework of how iron currently works, largely making it a truly cloudless compound. Rusticyanin would instead likely need to work as an organelle that allows you to directly extract iron from the larger objects, and as currently works, engulf the smaller ones. The more rusticyanin you have, the better you are at extracting more iron quickly.
Risks
- More competition over resources than other compounds.
- Iron chunks, so requires more searching.
- Reactive to oxygen - reduces with oxidation.
Rewards
- Relatively powerful and self-reliant energy source, as it directly converts to ATP.
- Securing a spot can mean you have enough energy to last an entire generation.
I didn’t cover thermosynthase, but if implemented fully as originally conceptualized, it would definitely be its own unique metabolism.