Modern UI version of IE11, has Flash included itself. That is all. You cannot install any other plug-ins.
To enjoy other plug-ins you need to start IE11 on the desktop environment. Any plug-in that does not work there are simply not currently supported by IE11. You may want to contact the company of the plug-in for a status update on this, or for a beta version which they are willing to share.
Firefox Beta has a Modern UI version available, but does not support any plug-ins. It can only play HTML 5 audio/video content.
Of course, the desktop version of Firefox support all the same plug-ins and extensions we came to know and love.
The problem with all this, is that Modern UI apps are completely sandboxes. As much as people praise sandboxing.. you have the mess that you have now. Microsoft needs to open up Modern UI apps to the "outside" to allow other programs to interact with it, and give you the ability to install plug-ins for it, and have the Modern UI apps be able to load them. Sadly, doing this, opens security holes.
It doesn't help the 'cause when you have Adobe doing a half job with their security protection with Flash, where you see exploits being used. So, it's a difficult balance that people needs to choose. You want power, and flexibility.... expect to live in a world of exploits, and the important of keeping your system updated, including versions of Windows (or Mac, or Linux based OSs), and live with an anti-virus solution. You want none of that... live in an enclosed environment, Apple'esk where everything is limited, and for an OS like Windows, you have this mix world.