This may sound minor but it's a big deal to people trying to cultivate trees. When you change to a saved base layout, if a new tree has grown in a place with a building's new location, the only options are to cut down the new tree or not go to the old base layout. Effectively this means that the base layouts don't work if I want to grow trees and I have to manually rearrange the base every time or lose the new trees.
The game could easily add the option to move the offending buildings, similar to how it moves new buildings that were not part of the old base layout and makes them flash for a few seconds.
I kind of want to quit the game every time I have to manually rearrange the base because of this.