The Ancient hologram in Atlantis mentioned a force as powerful as them. The series clearly shows that Atlantis' shield managed to handle the combined power of the Wraith's military tech, so the Ancients were obviously far superior technologically.
Now we know from Stargate the Movie, the Ancient Egyptians managed to drive the Gouald away from Earth. The only explanation for this was the superior numbers of the Egyptians and the Guaold had already established human colonies offworld.
So perhaps the Ancients were pushed back to Atlantis due to the Wraith's numbers. A hive like race would usually have far more numbers than one such as ours. Now when the Ancients were pushed back, they made the assumption that they were defeated. From the wraith posts on scifi.com, I get the impression that the Wraith didn't think they won the war. Each was making assumptions about the other. The Ancients, not being a warlike race may have just decided to return to more peaceful pastures, also with them experimenting with ascension, the Wraith didn't seem important anymore.
The Wraith clearly make a distinction between normal humans and the Ancients. I think that any battles fought between the two cost the Wraith huge losses for even a hive community to take, while the Ancients would consider the loss of even one of their people a terrible blow. The personal shield that was discovered could have prevented the Wraith from 'eating' an Ancient. So they were classed as the Great Ancient Enemy instead of just 'food'.