The ONE thing that made me move to CellProfile, besides the High throughput design, is the little tutorials everywhere with the "?" and the inclusions of references. I really like the examples and suggestions inside each algorithm explanation. Making an effort to make these explanations of the algorithm something more contextualized (with examples, situations that can be better applied, possible bad consequences) can be of huge help to lay people in image processing, and makes the program more self-teachable.
ImageJ. But I prefer Cellprofiler now. however there's one thing that is way easier to use in ImageJ: Manipulating images. EditingObjects Manually and such stuff are pretty easy there. But in CellProfiler, maybe because of the plataform (I don't really know), each drawing takes a lot of processing. I usually use ImageJ to draw my masking images in binary format and load them in CellProfiler. It was an option around the difficulty of drawing the ROI for example, in the image.
The example of clicking in the object and get its features would be awesome. Could make the "morphology-image metadata" relation that lay people (in img processing) find difficult a lot easier. Another suggestion is in the first question.
For CellProfiler, I think this is dangerous. It may take a person the drive to explore more, since there's a simple interface, or worse, deprive them of the possibilities they can have to process their images. I think that a great effort in a more exemplified or detailed instruction (in the ?s) could help.
Also, If some common processing (like the basic pipelines) could be described step-by-step explaining what they do in each (in general lines) and why they are necessary or desired, could help
When I started on CP, my biggest question was "What do I need to do with my Image in each step?" Maybe this "Simple version" could be a sub-interface, chart-flow based, asking questions and presenting the more appropriate options depending on their type of Image and need and etc. Each step would present a number of options depending the users need. This can take some options off the table, but would guide people initiating in a sense of teaching them what they need to (or can) do with their images.
Hope to have helped.