If NLS is enabled(the default) the waf script checks for intltool, which isn't declared. And pkg-config is needed too. The attached patch fixes this, and moves the runtime-only deps around. Thanks, James Reproducible: Always
Created attachment 181744 [details, diff] midori-deps.patch
Slightly related question about automagic: Is there a reason why the configure run doesn't test USE flags? It seems, to me, that the current ebuild shouldn't really have any optional dependencies as they are being used regardless of the USE flags if they happen to be installed.
Valid comment, updated deps accordingly, thanks for the headsup :)