Will NetLogo and NetLogo 3D remain separate?
No. The split is temporary. Eventually a single unified version of NetLogo will support both 2D and 3D modeling. We will be sure to design the 3D world support in such a way that it doesn’t get in the way when you are building 2D models. Models built in NetLogo 3D preview releases may require changes in order to run in the eventual unified version.