1. Being able to enable/disable popups and Java are primarily usability issues (to prevent annoyances), not privacy. Yet they are on a tab called "privacy". I would rename this to something that encompasses both.

2. Not being able to whitelist certain sites to be able to make popups and run Java causes the user to have to visit the preferences dialogs to enable/disable the options unnecessarily often. Also, it gets confusing when you have multiple tabs open simultaneously and you don't want to enable or disable the features for all of the tabs. In fact, it's nearly impossible.

3. The only way to set Epiphany to throw away all cookies when you close the browser is via about:config ? 

Other information:
Irrelevant for the bug report, but I am a new Epiphany user. I did not use it before because it was horrible to use (lack of adblock) but I have just begun using it and I actually like it over the Firefox already. Just couple tiny tweaks and it will be simply superb!