First, thank you very much for such a captivating game, that eat up over 30 hours of my life already

As for now - the thing I feel game lacks most is proper chemical industry. I've thought about modding but couldn't find a way to implement it with current set of entities. But proper chemistry should be added, you can't imagine a real factory without all those pipes going all the ways around it.
First, there should be a proper liquid(and gas) transportation and storage system. Pipes and pumps(with pressure physics included), tanks for storage(and a tank-cars for the train) and a way to connect pipes to processing plants(maybe chemical plants should have a buffer tanks of limited volume).
Second, a chemistry industry would need processing plants with not only several products for input, but also several products for output as well(e.g. processing raw oil will give as several fractions of oil, gasoline, and tar). Maybe this should be a more global concept, with all production plants processing some waste and scrap, that'll give more pollution if not processed properly.
And finally, new resources to process and different products to acquire. Oil, water(to get hydrogen and oxygen), getting nitrogen from air, underground ores and such.
Thank you.