There is nothing stopping us (the plugin authors) from properly categorizing stuff as you can see here (these are plugins putting stuff into a dedicated section):
Trouble is sometimes a plugin only has 1 or 2 settings and giving it a whole section is overkill.
The big thing I think I would like fixed is this mess, when you click settings:
/plugins?filter=affiliate
Instead perhaps:
?filter=plugin:discourse-affiliate
That way if a plugin sprays itself into multiple groups or omits a keyword in a setting the button will still work.
I guess when plugins register settings core is going to have to keep track on the server which plugin owns which setting.
I am slotting this particular change to our next release, cause it is small and makes a big diff.