Atlantis City has a Higher Purpose

[Dave]

When a alien bug attaches itself to Sheppard in "Thirty Eight minutes" it seems to have a reaction to salt water solution. That set me thinking. I wondered why the Ancients who looked much like us would build a very large city in the ocean of a waterworld. This bug was apparently an evolutionary distantly related cousin of the Wraiths. The Wraiths were the mortal enemies of the Ancients who eventually beat them. I wondered if Atlantis was built because the Wraith abhor salt water, and it therefore had a military advantage. Probably the answer is no, since I've read the Wraiths attack Atlantis later this season.

Atlantis definately had some purpose more than just being a city:

from SciFi Wire

Flanigan Sees Atlantis' Future

Joe Flanigan, who stars as Maj. John Sheppard on the SCI FI Channel original series Stargate Atlantis, told SCI FI Wire that the once-lost city of Atlantis will begin to reveal its secrets during the second half of the show's freshman season and on into the future. "On the overall level, what I want to see happen, and what will happen, is that the city of Atlantis is really remarkable," Flanigan said during an interview. "It's essentially what Manhattan would be if it were abandoned. If you can imagine the size of Manhattan and have it be just completely empty, it would take forever to explore that place."

Flanigan recently wrapped production on season one of Atlantis. "What we'll find out is that Atlantis actually serves a higher purpose, but it will take a long time for us to figure out what that is," he said. "And we'll slowly see the city come to life and start living up to its potential, and then there will be an ultimate cosmic purpose to the city of Atlantis. And that's a pretty interesting angle to explore. Of course, it's going to take a few seasons."

Anyone care to speculate on this?