FatTrucker: I don't disagree that it's fairly simple but most users are (in my experience) pretty clueless. The point is that in every emulator it is slightly different and in most cases the controller that is being emulated is slightly different. For a novice user, going into 12 different applications and entering 10+ buttons each time doesn't sound like a 10 minute job. I think it would be useful to have a single place where you can configure your controller, just like you think it's useful to have a single location from which to launch games for any emulator.
Thing is you only need do it once for each emulator. Once the controller is set up you're good to go for the future.
As far as a universal configurator is concerned, I don't think specifically that its necessarily complex from a coding perspective, more from the fact that, that code will need to address multiple different emulators that all configure their controls in different ways some coded internally, some via config or text files, some via drop down menu and some via external plug-ins. Then there's the fact that from emulated system to emulated system you don't necessarily want your controller set up in the same way, dependent on what controller you're using with the emulator and what the original controller was like for the system you're emulating. At that point you're into the territory of having multiple controller profiles per emulator, which not only defeats the object but is already supported in Joy2key and X-padder.
There are just lots and lots of variables and IMO it will be virtually impossible to automate it in a way that people will find user friendly or convenient across lots of different emulators and they'll end up going into the emulator config anyway to tweak the settings they want.
By its nature the emulation community attracts gamers of a certain type, and while some greener users can struggle with some of the more modern emulators for systems like the Wii and PS2, I think you'll be hard pushed to find many that don't have the basic technical knowledge required to go into an options menu and select 'Controller Config' then press their controller buttons to correspond with the on screen prompt to 'press the button for up' for example.
The whole point of a game launcher front-end apart from the obvious aesthetic improvements with screenshots and the like is that it allows quick and easy perusal of a gamelist and one click launching, its not the same thing as a global controller configurator at all.
From a more general standpoint, the emulation community has always been made up of a minority of interested enthusiasts, you have to ask the question should it really be made easier and more accessible for the casual crowd whose primary interest is simply in playing pirated games. Surely such things only serve to draw unwanted attention and counter productive PR to a community that currently receives a fair degree of unofficial support from the development community.
Taking Mamewah as an example, its incredibly convoluted and complicated to learn how to set it up initially, seeing off the vast majority of people who want to exploit it for gain or casual piracy. This prevents it from proliferating to a point where companies with commercial interests see it as a threat and kill it off.