Since create a patch is one of the most risky and tricky and annoying parts of the development, I think we really need some tool to automate it as much as possible.
FWIW I created a project at github for that:
https://github.com/elkarte/Elkarte/projects/4
at the moment I just added few thoughts, if you have any other idea feel free to ask.
This could potentially improve also the development of addons: you create a branch for each addon and then running the tool would create the package out of the "diff".
This should be good though I have no clue about it yet. :D
Yes, it's not easy.
The patch_to_mod script already does quite a bit:
https://github.com/elkarte/tools/blob/master/addon_scripts/patch_to_mod.php
converting a diff to the xml structure.
But is also the easy part. xD