Big thanks for your bug and improvement report again!
I'll definitely consider adding a panel which asks if a building should be placed or not and I'll care about the bug with the message panel.
The clipping issue is meant to be a function not a bug ; ) It prevents getting pushed into the universe when a new building and new colliders are instantiated near the player. The colliders will become active when the player moves away from the new building afterwards.
Yeah the terraforming can be quite heavy near rivers and mountains. But at least your workers won't walk into water. (Let's consider it to be the Netherlands function ;)
I'll improve the 3D Models inside the buildings for sure! In fact, I planned some dependencies on the supply with copper ware, furniture, wool, etc. just as you mentioned.
The water issue with the quarry is not solved yet. I have to think a little bit how to fix this, as the water level is global for the whole game and the quarry may go beyond it at some times.
The idea to make tabs for the research menu is good. I'll implement it in a version in the future. Returning some of the building material when destroying houses is a good feature, too!
For the saving function: I'm a little bit sorry, but this feature will first be implemented in the final version, or an early access version (I'm still not sure, if I want to support the idea of EA and if it is helpful for the development of the game, if the community wants to have one, etc)
You can imagine the saving function as a way to rebuild the entire game and then store it to some variables. As this is some work, I'll want to make sure, that the game runs stable before and the most bugs are fixed.