Thank you for the kind words!
To understand your first point correctly, you want a "beacon" that broadcasts in a configurable area "upgrade these buildings"? I'll look into it, meanwhile, out of curiosity, wouldn't the toggle option for blueprints to be upgraded and later upgraded if the stock in the base improves be to "anoying" to work around? Or maybe you didn't notice it, either way I'll look into it.
The second point I believe was solved by the module upgrade update. If not, please say so!
The third point I'll look into, I am currently implementing "passive" upgrades which would mean you can say "always upgrade prod 1 modules" or "always upgrade labs" or "always upgrade prod modules in lab with a priority"
The fourth point - There is an option to exclude and include modules when you shift drag over an area(and in that pass, exclude assemblers, so only the modules are targeted, and vice versa), is that enough or do I not understand your request correctly?
Again, I agree with you, this should be base game!
I am also currently making additions to the mod so you can request 200 mining drills, and then get x rare, y uncommon and z common, all adding up to 200, with highest quality being highest priority - and if the base then crafts another 2 rare, they will replace 2 common mining drills in your inventory.