My two cents ...
At my work, we typically use Aquaveo SMS to generate and improve the mesh, then export the *.2dm to Blue Kenue to generate *.cli and *.slf files. We do most of the preprocessing in SMS and most of the postprocessing in QGIS, as we find these programs more intuitive and easier to use than Blue Kenue, and more compatible with standard GIS file formats. Even then, because the newest publicly available version is 3.3.4 and this still has the apparent inability to write a double-precision .slf, this requires a coordinate shift, which renders it inconvenient. Most corporations do not want to install alpha and beta versions, so we are stuck with 3.3.4.
In all honesty, I would probably not use Blue Kenue, were it not for the step of generating *.cli and *.slf files. I find that the interface could be more intuitive, and there are plenty of small issues that I find frustrating. For instance, BK can only read rasters up to 24 bits, if my understanding is correct, whereas pretty much anything I use is 32 bits. I have never encounted this error anywhere else.
This is where I get controversial ... In my opinion, all of the hard work NRC is putting into CHyMS to basically create their own GIS platform could be redirected into adding features to QGIS, via a plugin or otherwise. QGIS can already interact with all sorts of geospatial data and read selafin files, and there are mesh generation plugins available. I think in the big picture, it would take less work to create a robust plugin than to try to untangle all of the years of legacy code in CHyMS, only to create a product that is similar to, but (in my opinion) less appealing than, QGIS. Again, this is not to disparage the hard work Alan and others are putting into CHyMS, because I appreciate the endeavours; all I'm saying is, the hard work could be redirected into an ultimately better product.
I hope this can help inform the discussion of CHyMS. Again, I'm grateful for the time you put into Blue Kenue, Alan - not the least how many times you've helped me understand bugs I've had - but in the big picture, I think it would be better for CHyMS to build onto quality, existing FOSS platforms like QGIS, rather than reinvent the wheel to support a relatively small user base.
Hope this helps,
André Renault