CMake is pretty established. You don't have to use CMake and if you don't want to, you don't have to use it - you can just compile your code however you like and manually put all your package files where ROS expects them to be, or use symlinks or some other hack. Doesn't seem to be worth it just to avoid CMake.
The build system is effectively almost required, though, because the documentation telling you how to do anything in ROS assumes you're using Catkin. I wouldn't know how to arrange files for ROS to use without going through the build system.
You actually can just cmake and that is all you need!
[in any folder out of source]
mkdir build
cd build
cmake [source folder]
make
source devel/setup.bash
roslaunch your_fancy_package demonstrator_nodelet_or_whatever.launch
That works, but you can't mix it with catkin_make or other build tools (rosbuild). I.e. you can't just invoke catkin_make there, this won't work afaik.
The source folder must contain a main CMakeLists.txt symlink which points to `/opt/ros/[distribution e.g. kinetic]/share/catkin/cmake/toplevel.cmake`.
This symlink will be created when calling "catkin_init_workspace". You can also just put a copy of that file there to commit it in git. I do this and even modify it to include my own cmake modules and debugging stuff.
You can now layout your folders any way you want. That means the packages don't need to all be in the same folder, but can be grouped as necessary.
You can put software components/packages in folders that are structured similar to project_utils / project_msg on any sublevel, I don't know what happens when you directly nest them though.. I wouldn't do that.