I think these three tasks need to be in the same application.
KXStitch is very good: I had a bit of a fight with scaling the source photograph, and another trying to print (I could not get anything to print, I have a colour printer, but it insists on printing black and white, the thread list is too small), some of the terminology is alien to me.
I think Liberty Embroider can follow in KXStitch footsteps. Templates can be generated from picture image files, embroidery patterns, embroidery designs, and in user-defined (or standard) sizes. The template layer is probably the first in the workflow. If the user seems only to select 5" by 7" (125 mm x 175 mm) and 8" by 8" (200 mm x 200 mm) hoops, then probably these are the hoops they have with their machine; and these could be offered at the opening template stage, but I think it would be better not to worry about how big the embroidery is at this stage and fit the design to the available hoops later.
The colour range of images can be decimated to match the available (or desired) thread colours, but again this should be a soft choice; perhaps similar coloured areas could use the same coloured thread or different. Fine detailing can remain for stitch direction hinting.
Standard thread colour ranges are available and part of the value of these things is having them available to the user, without the user having to fill in some tedious form. Imagine you scan or photograph the reel of thread/floss and the computer just reads the code number and colour name, and also extracts the red-green-blue RGB value.
Edge detection can guide definition of outlines and borders between different areas of the design/pattern. Built-in design rules can gently warn when the design exceeds the ability of the sewing machine or materials used.
Depending on zoom level threads or areas or patterns can be selected then manipulated: move (translate), rotate, and scale, as well as, cut, copy and paste. Patterns may also be added from external sources.
Text tools allow bitmap or outline fonts to be used and follow artistic paths.
Intelligently hooping large designs.
Thread resource management tool/database.
Pattern resource management tool/database.
Blank or Photographs → Pattern: colour optimise, edge detection (outline stitch), area fill (stitch colour and direction), resizing. | Patterns → Design: pattern scale/move/rotate, text font/colour/style/path