General

Keep data on the CPU side in a format that allows a simple memcpy to the buffer.
LOD models should store their different detail levels in the same buffer. The current level is then picked via index.
Models that are based on Nurbs should generate predefined levels of detail in a buffer. At some point, when the model gets really close, tessellation should kick in.
Complex models like humans should be modeled using patches for each region. For example a face consists of a nose patch, 2 eye patches, 1 mouth patch 2 cheek patches etc. The LOD of these patches can be dependent on the angle to the camera because the number of triangles gets most important if one can see the contour. The fragment shader handles the rest. The problem here is, that the contour is also important for shadow mapping which might see the model from a different angle. This might not be an issue or can be solved by reduced order models to some degree.

Possible classes

Scene class/struct that stores all the data of the scene (objects, camera position etc)

use interface blocks to pass variables between shaders https://www.opengl.org/discussion_boards/showthread.php/185141-Is-there-a-way-that-Geometryshaders-in-and-out-variables-have-the-same-name
Use 2D indexing of vertices to calculate a fragments position inside a vertex e.g. (0,0) for ll corner, (0,1) for ul corner (1,0) for lr corner and (1,1) or for triangles https://stackoverflow.com/questions/25397586/accessing-barycentric-coordinates-inside-fragment-shader
Use a map for Shader includes in some kind of preprocessor/includehandler class that stores all the includeable strings. Keys should be like a filepath to be compatible with includes loaded from files. Store keys of already included pieces of code in a std::set.
Notice there is a fragment shader derivative function https://www.khronos.org/registry/OpenGL-Refpages/gl4/html/dFdx.xhtml

General

(MAYBE) Store all objects of a level/sector with the same render setup in one buffer to minimize draw calls. Create a class on cpp side which stores all the objects. Even if there are different textures, this could work by adding a texture index to each object which picks the right texture. In the end there should be one buffer and one index buffer which controls which objects is drawn.

Shader programs

Use shader program groups - Creates the same effects for different primitive types or other properties (e.G. standard daylight rendering for triangles, quads, NURBS etc.)
Shader Program Groups stored by ID, not by name
Active Group ID always stored somewhere and passed to object during rendering
Objects store their setup for each used program group (ProgramID, Subroutine IDs, etc) to avoid searching their setup every frame.
Use the objects setup list to sort objects after culling and before rendering to avoid state changes