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Tested with GtkLauncher and epiphany. Plugin support doesn't seem to work with the GTK+3 version of WebKit ("Missing plugins"), but it does work with /usr/libexec/webkitgtk/GtkLauncher provided by the GTK+2 version. I noticed webkitgtk3 applies "webkit-1.1.14-nspluginwrapper.patch" while webkitgtk applies a newer, "webkit-1.3.10-nspluginwrapper.patch" version.
If you look inside those patches, their content is the same. Also, when I try to run epiphany, all the plugins load correctly (when talking about NPAPI based plugins) ** (epiphany:15890): DEBUG: NP_Initialize ** (epiphany:15890): DEBUG: NP_Initialize succeeded ... repeated several times. But I can not get your error, maybe more specific description would be helpful.
Test case: 1) Make sure gnash-plugin (or Adobe's flash plugin) is installed. 2) Use /usr/libexec/webkit/GtkLauncher (gtk2) and go to Youtube or some other Flash website. It works. 3) Use /usr/libexec/webkitgtk3/GtkLauncher or Epiphany (gtk3) to watch a Youtube video. Instead of displaying the flash content, the plugin isn't initialized and simply displays a "Missing plugins" error. I thought this might have been a Fedora bug but it's not. A workaround for the issue can be found in this blog entry: http://debarshiray.wordpress.com/2011/04/12/gnash-and-epiphany/. That link references GNOME bug #647516, which is a duplicate of GNOME bug #647096 and that in turn is fixed with a WebKit patch referenced there. I'll try applying that WebKit patch against webkitgtk3-1.3.13-1.fc15 and I'll report back here if I can get gnash to work.
Just to confirm: gnash works with the patched webkitgtk3. A simple update to webkitgtk3 1.4.0 provides the fix, but the patch should also be compatible with the version in Fedora 15. It can be found here: https://bugs.webkit.org/show_bug.cgi?id=58297 Epiphany must be updated to version 3.0.1 as well, 3.0.0 manually blocks gnash and flash instead of letting WebKit block the incompatible versions.
webkitgtk3-1.4.0-1.fc15, epiphany-3.0.1-1.fc15 has been submitted as an update for Fedora 15. https://admin.fedoraproject.org/updates/webkitgtk3-1.4.0-1.fc15,epiphany-3.0.1-1.fc15
webkitgtk3-1.4.0-1.fc15, epiphany-3.0.1-1.fc15 has been pushed to the Fedora 15 stable repository. If problems still persist, please make note of it in this bug report.