Of course, one needs to ask the question: Since skeletons and zombies are typically used as expendible shock troops for a necromancer or more powerful undead creature, is it necessary to worry about the transition from one to the other?
Personally, my thought is that the magic that animates a zombie keeps it steady at the point of decay it had reached when it was animated. If that's something not compatible with your concept of the mindless undead, it's easy enough to determine that the zombie has reached the point of critical decay and will now be a skeleton. Just remove the zombie template from the base creature and apply the skeleton template. If you want to know why skeletons function differently from zombies, it's because the agile and crafty skeleton inside the zombie has to struggle under all that stiff, dead flesh.
Well, that and it likes brains.