Thoughts:
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The manual harvesting of shepherd animals can be tedious. I know we’ve had at least one thread on this Auto-butcher When Pasture Full
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They’re currently reworking the building tools, and part of what was discussed will solve a lot of these issues. Stonehearth Dev Stream 267: Chris Continues to Conquer Building
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I get this one a lot too. If I decide to build a 1 x 2 wall even after the first one has finished the building, other hearthlings that were assigned still run up and give it a smack. I can understand why the system does this, you want something done so it assigns enough folks to make sure it gets done in good time. Problem is once the task is done it doesn’t cancel the order to the other hearthlings assigned to the same task.
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On the fence about this one. If the hearthling was going to say build something or place an item and my chest is in the opposite direction then the hearthling returning the wood/stone/clay to the chest before going to eat would actually take MORE time than just dropping the item closer to where it needed to be used. I definitely think they should drop items upon job change.
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I understand we all want more content, but we’re still in Alpha. They’re working on rebuilding some of the core systems, crafting is one of them. There will be more items and enemies added, just a matter of being patient.
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A fully leveled Engineer gets 8 turrets, I usually keep an engineer for each main entrance/exit to my towns and I don’t even lay traps. Enemies running into your city, under fire from 8 turrets, don’t last long even on hard mode. Anytime an archer has been able to hit my turrets, the turrets are able to fire back, but that’s with the level 3 turrets. The turnip shooter has a shorter range, they should definitely be replaced when you’re able to.
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Upgrade option for trade skills is a great idea.
8-10. On your list are micro-management issues. Personally I don’t find them to be a problem, this isn’t a game that just runs on auto. The door issue in particular is better the way it is, in my opinion. If I maintain 1 door in my inventory, then the door is already built and just needs to be picked up and replaced without having to wait for my crafter to gather the materials and then build the door. Speed can be crucial when replacing doors that serve a purpose for defense.
11-12. These issues should be fixed when the new building tool gets implemented.
13. Heh, yeah this one cracks me up. I personally love how the windchime works. If you’re scrolled out you don’t hear it, but if ya zoom in closer to it you can. The shepherd animals should be similar. The distance/volume of the effect should definitely be bigger than the windchimes, but could stand to be tuned down from its current state.
14. I LOVE this idea, then some of us wouldn’t have to resort to using console commands to teleport trees in from other parts of the map.
Your clerics are just making sure that poor starving poyo manages to make it till your shepherd brings em some food. They’re very compassionate those clerics. 
None of what I posted was meant as a critique of any of your ideas. Just tried to provide some links and other insights. You do have some great ideas here, and bring up some issues that can be frustrating.