The city of Atlantis, to the audience and to the Earthborn human characters, is all wonder, awe, and excitement. It is a place to explore and to enjoy.
Not so for many of the citizens of the Pegasus galaxy.
For the Wraith, the Asurans, and possibly the grey Daedalus Variations race, the city symbolizes the Ancients and their their genocidal campaigns, the captives who died in the prisons there and the genocidal weapons manufactured there. That anger was so great that it did not fade in Todd nor Oberoth, after 10,000 years, and caused both leaders to make jumpy actions (Oberoth wanting to destroy Atlantis just for vengeance and Todd jumping to conclusions about the who reactivated the Attero device.)
For the native Pegasus humans, the city’s technology means domination, such as “The Game” and “The Tower.” The fact that humans arrived from the Milky Way galaxy just means someone else wields power now, rather than the Ancients. Season 5 showed the New Lanteans being heavy-handed with the native humans. In “Identity,” John had used the city as a threat: “You know about Atlantis, right? Then you know you’re better off being our friend than our enemy, so why don’t you be our friend and show us where that terminal is?” Yes, John was under pressure to save Jennifer, but, in a season 6, this threat probably would have have led to more problems with the existing governments in Pegasus, such as they faced in “Inquisition.” The Genii and other Pegasus natives want to rule themselves.
Some of the problems the Lanteans face is just from living in Atlantis, that symbol of the Ancients and all its baggage. Being human in an over 10,000 year old family feud doesn’t help either and amplifies their association with the Ancients. Weir said the Asurans “look at the Ancients like parents who betrayed them, and now they see humans as the favoured siblings who receive all the parents’ love.” That’s not the New Lanteans’ fault, but that makes it harder on them, as other races in the galaxy might have the same feelings as the Asurans.
Living in Atlantis is political and it would do the New Lanteans some good to better reflect on that when interacting with all of the galaxy’s inhabitants.