Some of the frustrations with Mesh Baker have been due to limitations with Unity’s texture packer. Atlases must be a power of two which can mean wasted space in the atlases and the API requires that all textures be loaded in memory when calling the packer which is expensive and can cause MissingReferenceExceptions to be thrown for large atlases.
To fix these problems Mesh Baker will include its own Texture Packer. I have spent the past week working on this and testing is almost complete. Look for it next week.
I am also adding Show/Hide functionality to the API which only updates the triangles in a mesh and leaves the vertex layout unchanged. This looks to be about 4x faster than adding and removing objects from a combined mesh.