Get the bigger unit for sure. SWCG output is adjustable. With a larger cell, you'll turn the cell output to a lower level. The net result is that the larger cell will last you considerably longer. Regardless of the cell size you select, you're going to have to tweak that adjustment for your pool.

There is a point where a cell can be too big, but a 40k rated cell on a 16k gallon pool will be no problem. I run a 40k rated cell on my 12k gallon pool.

The only positive about the smaller cell is the smaller price.