I think @david488 you touched quite a bit of good topics. It would be nice to have cheap facelifts to allow for some special versions. I think it would be nice, if you could click “do not refresh the car” and the engineering of untouched parts would be for free. It would allow also to do a trick like first roll out sedan body, and once it’s done engineer more quickly a convertible/coupe variant. But is it worth implementing and with what priority?
About the factories, I agree that there is a problem, as I had very similar issues as you described. It’s very hard to make informed decisions with so many sliders. Like in 4.0 I’m leaving all of the quality control sliders at the default positions 
At the same time, it’s easy to end up with some weird situations where I have no idea what is being produced where at what cost and with what quantities. Maybe instead of fixing those problems via UI it could be simplified in someway.