The WebKit2 GTK+ API has always been GTK+ 3 only, but WebKitGTK+ still had a hard dependency on GTK+ 2 because of the plugin process. Some popular browser plugins like flash or Java use GTK+ 2 unconditionally (and it seems they are not going to be ported to GTK+ 3, at least not in the short term). These plugins stopped working in Epiphany when it switched to GTK+ 3 and started to work again when Epiphany moved to WebKit2.
To support GTK+ 2 plugins we had to build the plugin process with GTK+ 2, but also some parts of WebCore and WebKit2 (the ones depending on GTK+ and used by the plugin process) were built twice. As a result we had a WebKitPluginProcess binary of ~40MB, that was always used for all the plugins. This kind of made sense, since there were no plugins using GTK+ 3, and the GTK+ 2 dependency was harmless for plugins not using GTK+ at all. However, we realized we were making a rule for the exception, since most of the plugins don’t even use GTK+, and there weren’t plugins using GTK+ 3 because they were not supported by any browser (kind of chicken-egg problem).