If you only specify input and output files, Spine doesn't know what you want to do (export, import, pack, etc). The export settings JSON tells Spine what kind of export you want and what settings to use. If you are doing import (-r/--import) then you don't need an export settings JSON file. Also, it doesn't make sense to specify -i old.skel -o new.skel, probably you want the output to be a .spine file. If you want to convert from .skel to .spine use:
spine -i input.skel -o output.spine --import
You can use -r instead of --import (does the same). You can import multiple skeletons into the same .spine file. You can do multiple imports with one run of Spine, eg:
spine -i input1.skel -o output1.spine --import -i input2.skel -o output2.spine --import -i input3.skel -o output3.spine
Note older versions of Spine may not support importing into a .spine file via the command line. In that case you'd need to use the GUI, some shortcuts for that are explained here:
How to automate version migration of binary assets?
Unpacking your atlas files to individual PNG files can be done separately from converting your .skel files to .spine. files.
Once you have your .spine files and image files organized, you can use the command line to export them all. In the future, keep the .spine files and individual images, then when you need to export them all with a newer version of Spine it will be very easy!
