The new WKWebView export is designed for the new Intel XDK project format. I don't know if it works with the old format, but if you enable WKWebView, you must include all three of these plugins for it to work:
cordova-plugin-wkwebview-engine
cordova-plugin-file
cordova-plugin-httpd
If you disable WKWebView, you should not need any of them. If you use the new Intel XDK project format, or PhoneGap Build, those plugins are specified automatically.