They have their scope. It's a video transcoder. Programs are better suited to doing their job well rather than stretching themselves thin with loads of features.
Handbrake is great. But I would also recommend using Kdenlive. It is a video editor but if you just open your video in it and just export the project, you will get some good output format options.
It's easier to type a command than it is to add files to Handbrake one at a time. I can also run multiple encodes simultaneously. It takes 2-4 to max out my CPU depending on the codec and resolution.