The main improvement with Phocus is a full resolution preview. But that came at a price. With Flexcolor, the thumbnail images loaded immediately. With Phocus the jpg previews load quickly for initial editing of junk, but you have to then import them before further work.
Many of the Phocus advantages over Lightroom are designed for the integrated HD cameras ... like DAC, which only work with the H cameras/backs/lenses, but not the CFV.
Hasselbald experimented with a native DNG file format with the H2D/22 integrated camera (I had one.) In-camera compression slowed the capture rate and the DNG format was abandoned with the advent of the much larger 39 meg 3F files.
Many Hasselbald digital shooters agree that there IS a difference between 3Fs processed in Phocus/Flexcolor verses conversion to DNGs and use of a third pary RAW processor such as Lightroom. That difference is mostly in color rendition.
If you are Mac based, direct loading and processing of Hasselbald RAW files is possible with Aperture. I do not know if it is Hasselbald or Adobe that blocks direct processing of 3F in Lightroom/PSCS3.
Personally, when I have a lot of images to process ... like for a wedding ... I immediately convert all the images to DNGs, which is a relatively swift process in either Flexcolor or Phocus, and process in Lightroom or PSCS3. I think Flexcolor is faster for this task because you do not have to load the images to convert to DNG. However, you cannot go back to use Phocus if you open the files in Flexcolor.
I use Phocus because if there are some special images I want to get the most out of, I will go back and use Phocus for those.
For many automated functions, Lightroom is much faster than PSCS3 ... so is usually the software I use for these type of mass processing tasks.