Okay. In the context of the show, I think that Atlantis began to wake up the minute anyone with a gene walked through the gate, and proximity didn't necessarily count for anything. Once the city awoke, it could sense life signs elsewhere and open the doors appropriately, or turn on the lights, even though those lifesigns didn't have the gene.
In the context of reconciling this with the story, it could be argued that Atlantis only began to wake up with the unusual strength of Sheppard's gene, and then everything else came online accordingly as I said above. Without him there, nothing would have been activated to begin with.
What you said about air and heat above is a good point. Air shouldn't have been a problem - the city is big and I'm sure the doors could have been pried open to allow circulation. Heat, however, would have been a problem. On Earth, the bottom of the ocean is a mere 3C, and after 10,000 years, all the insulation in the city walls and shield wouldn't protect them from that. It is a temperature they could survive in, but it would be pretty uncomfortable. Bed-sharing for all, I'd say!
Re: part 2
In the context of reconciling this with the story, it could be argued that Atlantis only began to wake up with the unusual strength of Sheppard's gene, and then everything else came online accordingly as I said above. Without him there, nothing would have been activated to begin with.
What you said about air and heat above is a good point. Air shouldn't have been a problem - the city is big and I'm sure the doors could have been pried open to allow circulation. Heat, however, would have been a problem. On Earth, the bottom of the ocean is a mere 3C, and after 10,000 years, all the insulation in the city walls and shield wouldn't protect them from that. It is a temperature they could survive in, but it would be pretty uncomfortable. Bed-sharing for all, I'd say!