I agree there should be better ways of managing the factories. Since you played both games I'd like to hear your opinion on the non simulated nature of the prototype. Do you like the fact that you can start miniaturizing right away or do you prefer the simulated way assembly planter starts with? I've never seen any other non simulated factory building game before and it's kinda hard to judge how unintuitive this is for new players and if it's even all that fun at all.
Well the only real benefit I can see of not simulating the factories is that it will take into account the actual time for each machine to produce and the items to move on the belts. This is a little more intuitive than it just using the highest machine time and ignoring transport. So that would incentivize making efficient factories. But on the other hand I don't see any reason why you couldn't do that kind of thing inside the factory simulation. It might be a bit more computationally complex, but it would just be once instead of all the time when the factories are actually running.
I do like the fact that changing one machine propagates the change to every other instance of the factory, but again I don't see any reason why you couldn't do the same thing in the kind of factories assembly planter uses.
Also I don't know of any other games that do this kind of recursive factory building, and I would very much like too, but I do know the factorismo and compact machines mods for factorio and minecraft respectively do it.