TL;DR
Add a better way to get seeds from fruit.What?
Add another recipe with a much better chance to produce seeds, but with no other products.Why?
Currently seeds are 2% per fruit and each seed produces 50 fruit which is on average a net zero if you have no production bonus. However, Biochambers have a 50% production bonus which incentivizes using them for fruit processing... which then floods your factory with the products! Due to this, you cannot even start automating gathering of fruit until your factory is completely set up for a lot of throughput, and then you have to scramble to get nutrients in everything to start it up, and it's just a royal pain.If there was a way to produce seeds calmly without so much infrastructure pressure you could get a basic setup going that gathers fruit from your agricultural towers and turns it into seeds, allowing the player to see how much fruit the towers are producing and estimate how much throughput they'll need in their setup. It will ALSO allow a fallback in case your setup is incorrect and fruit starts rotting preventing creation of seeds. Running out of seeds is a failure state, meaning you have to go run out and find trees to harvest manually to get fruit to manually craft into seeds, and that's annoying!
In theory you can already set up something relatively basic by using assemblers instead of biochambers so you don't have to produce nutrients which greatly simplifies things, but you then have to use production modules and at least twice as many assemblers as biochambers, and the energy requirements for that are nontrivial on a planet where creation of energy is difficult.
