The GUI makes it easy to encode by providing profiles and a simple GUI, but offers extensive encoding options for people willing to learn and spend time experimenting.
Although HandBrake is pretty straightforward to use, you can adjust pretty much any aspect of your conversion if necessary. For example, when transcoding video you have the option of adjusting between constant and variable framerate, adjusting average bitrate and constant quality, having 2-pass encoding or not, as well as tinkering with encoder specific options, and many, many, many more options.
There are presets for everything, so you don't have to delve deep in to advanced features if you don't want or need to. And in most cases you won't have to because the presets are great.
There is no "pass thru" option when doing conversions, also there is no lossless option for audio when working in the video or HD video profile categories. Oddly enough there are lossless conversion options if you use the audio category, but this will output a separate file from the video.
Depending on the video container you use and it's capabilities, users can do separate conversions and then mux the lossless audio and video output files later with other 3rd party applications if lossless quality is that important.
In that case, this application would not be as convenient compared to other software, while it can do 1:1 copies, other software are more dedicated to this purpose and have more options in this regard.
Default profile options generally have most fields filled with "smart fit" option by default. This is essentially mirroring the source media as closely as possible, so you get a high-quality conversion with a mild (probably not noticeable) loss in quality.
Custom profiles can be made. There seems to be no lossless or pass-thru options for generic video or hd video profiles though.
By default, conversions use "smart fit" for almost all options. This amounts to nearly lossless conversions, or more accurately, high-quality for minimum effort lossy copies. By default, audio is compressed to lossy AAC format. Users can create custom profiles if so desired.
Video Converter Ultimate has great categories of profiles, some are generic video formats, generic audio formats, device specific formats including some virtual reality headsets which I have not seen before in other software, formats for editing in popular video editors, generic hd video formats, and for sharing over the web or for popular video sharing websites.
Buy it once and you're done.
They do have an annual license at $39.95 / Year and a Family lifetime license (2-5 computers) for $118.00. The $59.95 lifetime single license is a good deal if you think you'll use the software extensively beyond two-three years.