First, I want to say that I've read a few other suggestions on farming and eco-friendly power and hope I provide enough of a spin on it. I've played around 50 hours since the Early Access release and I've completed all of the milestones except for 100% of the alternatives.
Second, I don't think that the basic biomass generator should be automated. I enjoyed the progression between loading biofuel into a handful of reactors until I could finish a 300m conveyor belt from a coal mine on a mountain, so I wouldn't want to take that away. I do think that biomass/biofuel should have more of a future than being left behind permanently.
One things I enjoyed most was the secondary objectives provided by studying caterium ore and the resulting materials, even if it ends up feeling more required because of all the advancements it provides. I believe that eco-friendly machines would make for a great branching path at or around tier 2-3, starting with wind power like a lot of others have suggested. Wind power would likely start with Rotors as a primary ingredient, with an upgrade at Motors, and Solar Power would probably use Caterium.
That would provide alternatives to coal and possible to early oil, but I think that for balance eco-friendly power sources would take more space for less power, and be materially expensive. The trade-off would be having power sources that could stand in open areas without conveyor belts and mining equipment feeding fresh resources in. You could also argue that since solar and wind doesn't have a 100% generation up-time, it's held and spread out to avoid lowering overall power generation. They would have constant power generation like the current geothermal plants too.
That brings me to Hydroponics or auto-farms and biofuel. Once I hit around Tier 5 and had to explore across the world for oil for the first time, I had pretty much leveled the local area of flora in order to automate construction while I was gone. Wood and leaves were not only useless, but I had 1000 biofuel I hadn't touched since my coal generator went in. I didn't unlock fabric until well after this first major adventuring phase, and it only has one or two uses. Even if there was a use for biofuel I wasn't going to go out and clear even more trees after having landscaped my hub area to death.
I imagine it like this: A Hydroponic farm can either grow a green leaf version or a mushroom version. It requires a lot of materials up front - wood, leaves, mycelia, berries, nuts, etc, as well as frames, computers and maybe even an AI limiter. At the least the natural resources could be replaced with the appropriate biomass and some of the healing items. The farm would take up a sizable area, 3x3 or 3x4 on foundations, and would be an enclosed bubble with an automated farm you can watch run (but it wouldn't have to be very complicated movement).
Each farm would then have a conveyor out or two for harvested materials (healing items, mycelia, leaves, flower petals). I'm not sure if there's a use for wood outside of just biomass, and having a separate biomass-out might unbalance power generation. Regardless, you'd need smart splitters in order to separate what you wanted for biomass and what you wanted to store or refine (for fabric, inhalers, etc). Otherwise you'd have to hand-pick over the output, which is fine until you figure out efficient automation, I think.
Having automated access to basic healing items at this point seems pretty fair. This would be after you've found oil, but before you'd go out seeking geysers. Scavenging is fine (and fun) but that's only from a single-player perspective. If I had 3 friends playing with me, healing items would start to feel more and more rare. Certainly I'd like a way to mass-produce filters by the time I'm Tier 6, since those gas zones are all over the place and you burn through filters unexpectedly fast while exploring alone.
So where do you put all of this extra biomass and biofuel you're generating? Fuel Generators. Either let them run on biofuel naturally (at a higher use rate than oil fuel), or make refineries that turn biofuel into biofuel+ that also runs Fuel Generators. I don't think an entirely new machine has to be necessary, since I'm already discussing a half dozen new assets. The new biofuel+ could also be an alternative for oil in plastic and rubbers, more expensive to start up than just getting oil but not requiring transfer from a far-away position (I say this as someone who had fun building 3km of Mk. 4 conveyor belts to tap into an oil resource).
The real cost of being eco-friendly would be the amount of space and resources you'd need to start it, but it'd be pretty cool to terraform the desert into a giant bio-fuel production plant with a dozen massive hydroponics farms feeding into refineries and generators.
Overall, the branching paths would look something like this:
Tier 2: Rotors feed into wind power.
Tier 3: Caterium feeds into solar power.
Tier 4: Motors feed into better wind farms.
Tier 5: Computers and electronics unlocks Hydroponics
Tier 6: Biofuel refines for Fuel and oil alternative, and Geothermal comes in as another eco-friendly option.
Never do I think that coal and oil should be removed from the equation. You still need coal for steel and oil should always be the more efficient choice. However I do think people would enjoy having the options, even if there was an uphill struggle to run on a purely 'green' energy, to the point where it might even be a bit of a challenge run to do it exclusively towards the end goals.
Tl;dr: Branching paths with green energy options, lock farming behind computers because you're no farmer, reintroduce biofuel as something useful, suggest all this with full knowledge of the amount of work it'd take the devs to incorporate.
Thanks for reading!