In older versions of epiphany, when I downloaded a file I was asked whether I want to open it in the appropriate handler or save it to disk (which would prompt with the Save dialog).

With the webkit backend, this no longer happens, and all files behave as if I pressed 'save to disk'. This makes it more annoying to do view files that I don't want to permanently download, but just view. For example, before I could click a link to a PDF document and press Open to view it in Evince; now I have to pause and think about where I want to save the file, then minimise Epiphany and activate Nautilus, then remember where I saved the file and navigate to that directory, then locate the file in the list of files, then open it... it's a lot more annoying now. :)