I have the 14 Biocube and now the 28g Nanocube LED
Just out of personal preference, I prefer the full canopy of the Biocube covering the filter area. Since the Nanocube has that open back, it has the potential to allow dust and other atmospheric "contaminants" in. I just set up the first Nanocube for live rock curing and am working on a cover for that open filter area.
The nanocube does have a better viewing window in the back..you can see all of the chambers vice a small bit of the filter chamber in the Biocube (chamber 2). Minor, but I like the larger overall view. I can see the pumps and if there is anything interfering.
As Joy pointed out, the cover weights are much different. The Biocube is lighter and is attached using hinge pins..it makes it harder to take off if needed but I think is more stable. With the Nanocube, the canopy just snaps in to the hinge plate. While it makes removal and re-attach easier than a hinge pin, I can just see those little tabs breaking off. Better to unscrew the little screws holding the hinges then popping the canopy on and off. Granted, you wouldn't be removing the canopy that often but it did make the initial rinse out (manufacturing and travel dust) and placement of the liverock easier without the canopy in place.
The BC has two intakes from the display area..one at the top and one at the bottom, that flow into chamber 1. The nanocube has a single, top centered inflow which empties directly into the middle chamber. Looking at the circulation of the two return nozzles, it forms sort of a circular pattern top to bottom rather than left to right, with it flowing away from that intake. I played with the direction of the returns but for the most part it was the same. Not sure how that will help with removing larger particles of detritus.
I did a lot of upgrading to the 14 BC so it barely resembles the original other than shape and size. At least with the 14, the return flow isn't the greatest..it is better to upgrade the pump to at least a Mini-jet 900.