but I only need management tools with browsers to control IE-specific settings like trusted sites, compatibility lists, active-x settings, etc and only for IE-only websites that use that junk.
Other browsers "just work" as they're build on universal technologies that really don't need a "trusted sites list" or a 3 page document on a very specific active-x setting list to make some ridiculous feature work.
Fix your web apps. This culture of IE-only built apps only causes more security woes and more administrative headaches than needed. Sadly, its still 1998 in the corporate world.
That's fine and all but I need to have something that can run in a browser and communicate over a serial port. My two options there are an IE plugin/extension/addon or a Java applet. Personally, I find that writing an addon in C# to run in IE is the nicest, cleanest solution even though I generally dislike IE as a browser.
Pardon the vagueness.. but, this use case was a hosted web app, so it only exists in a browser. Some customers required the use of driver's license scanners in order to expedite their business process. Not using Active-X or something like it would've meant writing a whole new fat client UI for the group of users that needed the DL scanners. The simpler solution is to write a little shim and have the native code populate the previously existing form fields. Aside from feeling a little bit dirty, it worked pretty well.
How about anything. Try configuring browser settings in Firefox or controlling a Chrome updates. It's a mess.
Chrome sort of has group policy management, but it's buggy. If either browser had an API, IE would fade away -- this is literally the only reason it exists.