Again, no surprise that these two cultures living in such proximity would both have a flood story to panic their descendants with. In literature, water often means rebirth and renewal. And, we at Shmoop, guess you could say that a massive flood that wipes out every last human (save for Utanapishtim and his wife) could qualify as a renewal.
But, it is also important to remember that the Mesopotamian cultures relied on those two rivers that they were set between (remember that Mesopotamia means "between two rivers"). Those rivers often flooded—which, actually, was a good thing: it meant that the silt left behind would provide rich soil for crops. So, in a sense, the flood story that Utanapishtim tells is representative not only of the purification of humanity (read: the gods starting all over again with humanity) but also their rebirth into a new, better, richer world.
In fact, we even get some actual birth imagery in Utanapishtim's description of the Flood: "Six days and seven nights came the wind and flood, the storm flattening the land. When the seventh day arrived, the storm was pounding, the flood was a war—struggling with itself like a woman writhing in labor" (11.127-130).
And yet, on the other side of it, Utanapishtim and his wife receive immortality and a new race of humanity is born. (Okay, that last part doesn't actually make it into our epic, but since there's a Gilgamesh, we have to assume that somewhere along the way people were created again.)