Woah, settle down HalcyconSky! The first time I've talked to you in ages and this is your post? No hello or anything?
As I've already briefly gone over, I don't really find the God of Gaps theory all that much of a problem, certainly no more of a problem than the science-of-gaps that I see being proposed all the time.
Whilst I understand how you see the similarity between earthquakes 2000 years ago and how creation is seen today, there are a few differences. The first is how far we have come scientifically since that time. Yet still, under the standard model, the beginning of the universe seems to violate naturalistic explanations. Thus, I have no problem supposing a supernatural explanation where naturalism fails or has very little explanatory power. It could also be argued then, that just as how technology improved since 2000 years ago, so it will continue to improve until we show that there was a naturalistic explanation for the universe. If that ends up being the case, then fantastic - another mystery under sciences belt solved. However, to assume that an answer will be found and indeed, that there is a naturalistic explanation, seems just as naive as the cave men you were describing - it presupposes the truth of naturalism.
Would you care to put forward the model (or scientific theory) which you believe is the most plausible and solves these problems?