1) ffmpeg is a good tool, only that its a cmd-line interface. not GUI (graphical user interface)
the GUI version of it is called Winff
Although its fast too, I'm not sure if its 'faster' than your existing FormatFactory.
2) HandBrake, is also a fast tool as well. Many comparisons state handbrake to be faster than FormatFactory.
It too offers almost all the features of FormatFactory while being much faster.
Yeah, all the convertors are just frontends for ffmpeg, so if you learn how to use that you can do anything. Handbrake included.
The speed and if it uses the gpu all come down to the settings the front ends use.