Scrapings prominence
If you were to ask me what I thought was the worst part of the game I would say scrapings utility for success being so mismatched with how low its prominence in the UI is.
Not only can this make it annoying or confusing to use but for new players psychologically makes it seem like something you shouldn't do even tho its important.
I'm no game designer but what I would do is put a toggable button with clear symbology conveying the idea of scraping near the upgrade HQ button.
When turned on clicking on a building would scrap it and trying to place a building on top of another building will have the game scrap the underneath building then place the new building in one move.
The following is probably going to be more controversial but I would change the scraping patent to decrease or remove construction time instead what it does now.
Then I would have scraping be a 50% refund that all players get by default.
This to me would make the flow of the game feel better.