I read a post debunking the stigmata in part because it first occurred (at least in St. Francis' case) on the hands instead of the wrists. The writer also asked why it took thirteen centuries to happen, etc..
My two cents is that God is not static and is constantly capable of surprise with the single constant goal: winning our love. Thus, it doesn't surprise me that for 13 centuries no one received the stigmata since cultures are so different that something that might repel one culture might attract another. The stigmata spoke to that medieval culture in a much more powerful way because that culture valued the wounds of Christ more, having had the luxury of centuries of reflection and meditation on the gospel. It was a gift to that culture. That is not to say that the middle ages were necessarily "holier" but just that what moved the holy was different. For God to have caused the stigmata on the wrists would have made no sense to medieval people and thus would not have effected His ultimate purpose - to motivate us to love him, not to provide scientific evidence.
It's not surprising that Jews near the time of Christ, for example, might've mis-read who Jesus was since they understood there was only one God and G*d surely wouldn't stoop to the level of not only allowing himself to be named but also possessing a human nature. Yet the Cross was a dramatic gesture that motivates millions to a greater love of God, since a God that suffers for us is a God much more easily loved than a more deistic one.
Bottom line is that for those open to God, he responds - in the now and 'just in time' (although he is outside of time) - to what moves a culture, if they ask and our receptive.