you don't have to fill your tank to capacity if you're concerned about weight or water quality, even though on a larger boat (50, 60, ...) a few hundred pounds dont' make much of difference. But it's nice to have the capacity.
i also cycle my tanks, i never connect to dock water.
an other issue with watermakers, although i've never had one, is that they can only be run in nice clear water... it's my understanding silt will drastically reduce filter life and any oil/contaminant can ruin the membrane.
i just think that on larger boat, you want flexibility. Water capacity, adequate ventilation, generator vs inverter, etc... as boats go up in size, so do the owners/guests needs. I believe that as small boat builders expand into building larger boats there are more likely to keep the small boat mind for a while.