3D Rotate command does not use the user coordinate system - Solution

Issue:

You want to rotate a 3D Object along the axis Y of the User Coordinate System (UCS), but the Y axis of the World Coordinate System (WCS) is used instead. 

Causes:

The command defined to rotate 3D objects is 3DROTATE. 
As designed, it is recommended that you use the gizmos available through the 3DMOVE and 3DROTATE commands to manipulate 3D objects. 
By default, the World Coordinate System (WCS) is used to Place the gizmo.

Solution:

Relocate the Gizmo: 
Right-click on the Gizmo symbol will display the context menu allowing to relocate and align the Gizmo with the coordinate system of your choice: 

 

As an alternative, you can use the command ROTATE3D instead. 
This command allows you to define an axis of rotation. 
The axis of rotation (X, Y, or Z) defined is aligned with the current User Coordinate System.