Oh I want to reply to so much of that. Let's break it down.
Make it so the mines never reset and monsters never respawn
I would be okay with them resetting just once each morning actually. That way, you can leave loot behind on levels you already cleared and run back and forth hauling that stuff out to your chests in the entrance.
The elevator in the mines requires spending 2 million to fix because it's a hazard and just going deeper wouldn't make it work again
One could argue that each 5th floor has to have a circuit breaker reset to enable power to the wall lighting for the next 5 floors as well as powering the doors to the elevator for that floor. Or maybe there's a debris obstruction that needs to be cleared from the shaft that you perform 5 floors at a time pulling debris out at the elevator door on that floor (everything in between settles downward to your level).
Make all crafting recipes take time to craft, up to 10 hours for stuff like crystalariums which you can also only craft with help of Maru or Demetrius.
I like this idea. I had married Maru on my last run through and wondered why she always talked about automating the farm more but never invented anything unique to help with that. She could have made something players have been asking for, like a machine that complements the hopper and works like the auto-grabber only it grabs from machines within 1 or 2 tile range to put the items into it's own storage. She's a nurse by occupation, which seems strange, but maybe some story line where she opens up a hobby shop or something to run repair services on machines and help with advanced construction. I mean, if Penny can get a new house built, why not?
Let's remove all stacking functionality from everything, doesn't make sense to carry around a bunch of stacks of stuff
Maybe the back pack can be given fewer spaces or every item has a volume to use in storage management and we can have wheel barrels, carts, and the like. That would be fun. Hitch up that horse to pull a plow even.
You will lose health if you hold radioactive ore or bars or anything crafted from them
I'm actually curious why this isn't already the case. The ore needs to be given a name though, like Uranium and there would need to be extra equipment slots for things like protective gear. I play Satisfactory once in a while too and this is the case. Toxic gasses as well in that game.
Chests only hold like 10 items and none can stack, if you have a big item like a furnace you can only put a single one into the chest
You kind of repeated yourself on this one.
Using furnaces lets off toxic fumes and after a while smoke fills the farm so you can't see and you lose health constantly as well as getting fines in the mail
Smoke is cleared by the breeze but there could be a limit to how much smoke can be cleared each day to give it that ambiance? We could even add a locust event forecasted as weather like the green rain is and the farmer would have to set up fires all around to create smoke and sway the locusts away when they come the next day.
Animals make the mess they do and require constant washing and cleaning of their coop, the outside area, etc.
A source of fertilizer other than bones and bug guts. Fruit Bats would also drop guano for the same effect. I can see that working its way into the game.
Every time you break a machine it breaks into about 50% of the composite materials used to craft it - if you hit something with a pickaxe what do you expect?
I think this was provided as a way of communicating your intent to pick the machine up rather than interact with it so you don't have to use additional buttons.
You get fines for littering and placing anything anywhere
The town would need a police service to catch you. I think people in such a small community would just assume you were intending to use the item where you place it, or retrieve it at a later date and not care. I put decorations in or around people's houses all the time since I have no need for them in mine and you can't sell them.
You need to get permits for making any building on the farm and get at least a few health inspections on the farm yearly
One could argue that the gold you pay for construction covers that since only one person does all the building. The mage doesn't build really. He materializes new buildings. Nobody is going to challenge him for fear they will have their house disappear in retribution.