I've been working on a site that will generate config files for you (Mostly for my job, but as a side project), and I've just "finished" one that will create a permissions file for PermissionsEx. I intend on adding others, like EssentialsGroupManager.
It may not be the most intuitive site, because there's a lot of stuff you can enter, but there is no order you would need to enter anything. You can do worlds, users or groups first, and attempting to add a user to a group before you've created the user will create the user for you. Users you've created but not added to that group will populate the autocomplete for the box to add a user and the permissions section will populate from a list of permissions that previous users have entered on the site. Obviously, that list will be pretty empty at first, and I have to approve permissions that have been entered to be allowed in that autocomplete to weed out "tests" and inappropriate entries.
It supports permissions per user, users being in multiple groups, world-specific permissions per group, inheritance and plenty others. I'm not super familiar with PermissionsEx and the wiki's Advanced guide and Basic guide contradict each other a bit, so if there's something not working properly, I would like to fix it up. You can also save what you created, to share it with others. I may add the ability to download what you added as a file. The script may be fragile, but it's held up to the limited testing I've done.
I only extensively tested this in Chrome and had help testing in Firefox. IE 9 definitely isn't supported, but beyond that, I'm not sure what other browser it works in. My jQuery experience level is... "experimental".
In any case, it's ready to be played with. If you have any questions, or manage to break it, please let me know.