On the whole yes 3D cell culture is better than 2D cell culture. When cells are cultured on traditional flat surfaces, the cells are forced to flatten and change their morphology in order to grow and survive. This requires a huge adaption in shape and function and these cells now no longer represent in structure or functionality the same cells that were growing in vivo. So when studying the function, architecture or response of a cell to stimulus / drug, 3D cell culture can help gain a better understanding of the natural in-vivo response.