In looking over nut samples from this year's nut evaluation, I noticed a particular pecan shell characteristic that seems to limit percent kernel. Its not what you might be thinking. Yes, shell thickness is obviously an important determinate of pecan shell-out percentage but the shape of the shell can also impact percent kernel. Take a look at three seedling pecans (photo below).
These three pecans share a common pecan shell trait; they all have an extended apex (marked by the bracket above). The extended shell apex looks like the hand of God just pulled on the tip of the shell and stretched it out. Inside a pecan's shell, the kernel is oriented with the connection between the two kernel halves (and the seed's embryo) closest to the apex. When the apex is extended like the three examples above, kernel doesn't grow up into that region at all.
Here's a photo of a St. Genevieve nut that I've carefully peeled away the shell to reveal the kernel (at right). I placed an uncracked St. Genevieve nut in the photo for comparison. Notice that the entire extended apex of this nut is composed of shell and packing material. The kernel starts well back from the apex.
Even if a nut has a thin shell, the pecan that has the extended apex characteristic produces a lump of heavy and unproductive shell at its tip. Pecan cultivars that share this shell shape usually produce 44-48% kernel. Cultivars blessed with exceptionally thin shells and cursed with an extended apex will produce 50% kernel at best.
Other cultivars that share the extended apex trait include Goosepond, Colby, and Niblack.