There are two main ways to cut boards - quarter sawn and tangentally sawn.
-Quarter sawn is generally regarded as a superior quality. If you looked at cross-section of a trunk, the quarter sawn boards are the radial ones (like the hands of a clock) You can only get so many of these from a tree. The grain is very straight/close together (because it goes right over the rings of the tree from inside to outside), and they will tend to be more stable.
-Tangentally cut boards are the ones left over, the ones not radial, but at a tangent (hence the name) to the radius. These have a more open, wavy grain, as there are fewer rings over the length of the board. These are more prone to movement.
In terms of quality for necks, I'd guess that the quarter sawn, being more consistent in structure and less prone to movement would be the superior choice. Make of that what you will - if your observations are correct, it's possible that companies are increasingly using tangentally sawn wood because it's cheaper and more plentiful. Possible, but far from definite, in case any of Fender's lawyers are reading this!