Just a quick note at the start, since I’ll be using official definitions: The terms autotroph and heterotroph refer to whether an organism can make its own organic carbon (In Trive terms, glucose) from simple stuff like CO2 or can only use already existing organic compounds, respectively. If you’re talking about divisions in how an organism collects energy, the terms to use are chemo-organotroph (breaks down organic carbon compounds for energy), chemo-lithotroph (energy from non-organic compounds) and phototroph (you know this one). Wikipedia has a neat little table.
That means in Thrive right now, the organelles that let you be autotrophic are the thylakoids and chemosynthesizing proteins; and in eukaryotes chloroplasts and chemoplasts. The Iron oxidisers and thermosynthesizers are not (which also means the name of the latter is not really accurate).
This is kind of a shame, because it means as a predator eating these last two types is not all that useful, unlike eating the glucose filled real autotrophs. They’re more sitting alongside the rest of the ecosystem, rather than being closely connected to it. Producing glucose would also store the energy in something that is not ATP, allowing it to be shared between cells in multicellular organisms, and lasting between shortages of the energy source, like spaces between iron chunks and lack of favorable thermal gradients (in the future).
In addition, in real life cells need a lot of organic carbon to grow, perhaps more so than phosphate and ammonia, which would be like Thrive requiring glucose for growth and reproduction. This can maybe be abstracted away in the cases of the real autotrophs (which produce a lot of glucose all time) and chemo-organo-heterotrophs (since they will be eating a lot of glucose which they use for energy anyway), but your iron and temperature dependent cells would realistically have to be eating some glucose in addition. This is not strictly necessary for a game, but I think it would add to the educational value.
Now, how could you go about improving this system? I broadly see three options:
The boring option
First option: just make thermosynthesis and rusticyanin produce glucose and ATP. Sure, that improves some aspects but it is not very interesting, and I think it reduces variety overall. Also, while it may seem wacky, cells that use energy from inorganic substances such as iron (or even light!), yet still can only use organic carbon made by others do exist. So, it would be a shame to lose that possibility.
Use the upgrade system
The current organelle modification system or any future upgrade system could be used to switch between producing ATP and glucose. While at it, might as well expand it to light and hydrogen sulfide! This would increase variety, rather than decrease it. Unfortunately, I have no idea how difficult this would be to implement into the modification system.
A third option would be to add carbon fixing proteins as a separate organelle, producing glucose from ATP. There are several pathways for this, but on Earth the most common one is the Calvin cycle used by the plants we all know and love. This might actually be the most “realistic” option since carbon fixation ability is separate from energy source. From a gameplay perspective this also allows you to match the capability with any energy source you choose.
The downside to this is that there would have to be either a manual switch to turn this off, or the process should only run if there is an excess of ATP, since you don’t want to run out of ATP because your carbon fixation is taking everything. A wasteful ATP to glucose and back cycle would also have to be avoided. I consider this the most complicated option.
In the latter two options, I would also suggests that the chloro-, chemo- and thermoplasts do directly produce glucose instead of ATP, since on Earth the carbon fixation takes place inside the chloroplast. This also makes from the perspective of -plasts originating from a autotroph being engulfed by an otherwise heterotrophic eukaryote.