I rationalised the expedition failing without John and his gene in particular: we know his is the strongest, or that he is most able to use it on an instinctive level. In 'Rising' we see the city responding to him specifically (the steps lighting as he goes up them) but not whether it responds the same to any others with the gene, and it was plausible to me that it didn't. Once I assumed the city didn't come on - they're not using power, so the shields don't start failing, so they don't need to go to Athos, so the Wraith don't wake, etc.

I like your idea about a change to Rodney's perspective; I didn't think Rodney was quite right (he felt turned up a few notches), and it would have been interesting to see him from inside.