This isn't THE only issue with FFMPEG. There are many many problems with FFMPEG, but it's the best thing we have in this area. Warts and all, I would probably, no, definitely would not have been able to achieve many of the career accomplishments I have without it.
As you start to reveal the multitude of switches/options/etc available to FFMPEG via GUI, the GUI becomes gnarly and complicated very quickly. This then becomes just as daunting to the avg user as trying to build the command itself. There are many practical uses for a very simplified GUI to achieve a limited set of functionality. There's nothing wrong with it. In fact, I'd be willing to guess that if a UI came along that exposed every single thing that FFMPEG could do, fewer people would use it than a much more simplified version.