The points you bring up can certainly be a limitation. One solution to consider is to limit the amount of data being analyzed. For some applications, analyzing a max projection of a 3D object might be enough to answer the questions being asked. The max projection is the representation of all the confocal images of an object stacked into one image. This requires a lot less time to analyze compared to looking at all the individual z-stacks.  Unfortunately, the technology is not quite there yet, but it is getting better. 3D image quality is improving and getting faster, with features that allow for pre-scanning at lower magnifications to identify objects of interest first before moving to more time-consuming higher magnification imaging. Limiting high resolution images to an “as needed” basis is another way you can reduce data collection.