Ah, funny idea. In most cases we would be talking about the species, not the individual dragon. If the Silurian dragon indeed lived 30 millions years before the Devonian dragon it would have had enough time to gain more skills than the Devonian dragon. However, that means the 2 dragons are in fact not the same. They are more like, different lines, not really upgrades of each other.
About those old creation stories.. I think people wrote some powerful beings must have existed to create something like the earth. However, they fought amongst each other, so they died. (Gods, titans, Ragnarok and stuff) Not saying every God died, but in heaven you would not see them anyway.
And we can see in evolution that ''Small + fast reproduction = win'' ''Big, slow and eats a lot = tricky.''