Okay, so we've got the three factory types, and some rudimentary production line capabilities.
Personally, I love
Factorio, I can sit and play "build an automated system so that it plays itself" all freaking day long. The idea that I could play Starmade as a "Set up this ship to go mine, bring it's raw ore over here to have it processed, then load that into this place over here for storage, then have this place over here running a factory to make X that pulls cargo runs from storage" blah blah blah makes me happy. I could play "build an interstellar supply and demand infrastructure" and be happy.
Having multiple types of factories that used different numbers of inputs so that getting a final product produced automatically required a planned setup would be great.
Failing that, I'd rather see factories simplified so that its a glorified crafting station from Minecraft where basically the one factory can do everything.
Right now the basic/standard/advanced seems like just an arbitrary split along arbitrary rules. All the same thing, just with different recipes in them.
Frankly, its really just middle road enough to make me frustrated. Its just complicated enough to make me want to do much more with it, but still simple enough that I can't really do more with it unless I just pretend that it has limitations.
So yeah, for the Universe update, I'd personally like to see factories get a LOT more complicated, or a lot simpler. This middle ground approach is just kind of clunky, IMO.