Make project files exclusionary vs inclusionary
I'd like solution explorer to be a view on the file system. By doing this project files would be incredibly merge friendly, because they would only be updated for metadata (prefer many files to one file with many sections in that case too) or exclusions. This might open the door for more convention based project configuration/structure than even today.
This will also help with the nasty problem of csproj merge conflicts because of high churn.
Think of this like .ignore files for Visual Studio rather than .includes. You add more often than you ignore.