Oh, congratulations Luke, your software is now part of the establishment. It's well deserved.
To just follow on a proposal.
W2E uses three places of real estate on the front panel. Some people can resent it and find it a little confusing. I think one would be enough.
What for a solution like the one on the photo (the image is optional), I mean
- Only one button which opens a "W2E Preferences panel".
- On the front panel, a "proceed" button to press just to create the epub
- Some tabs, metadata, structure, splitting, whatever suits your needs to provide the user with some choices.