Another problem I have with Negatron is that while the author says its operation is intuitive, I must judge that our intuition is somewhat different, as I find I need to refer to the documentation, quite often, to do even the simplest things. Setup is a breeze, though, compared to QMC2! It's plug-n-go.
I agree with you, Negatron is NOT intuitive at all!! That's the point that led me to stop using it really quick. QMC2 and LaunchBox on the other hand are quite intuitive, as soon as you get used to some specific behaviors on each one of them.
At this moment I'm trying to use LaunchBox and I'm enjoying it, despite the fact that you have to use commandline parameters manually to every single game you have in your collection. This is kind of annoying but fortunatelly, I don't have many games/systems in my collection. However, if you have a huge amount of games/systems, you will find LaunchBox very painful to configure.