Treatment of Teyla is pretty demeaning. Starting from the blatant sexism in the very first chapter is not very encouraging of the beginnings. And all of it, for what?
If I read the phrase "mitochondrial DNA" one more time, I will hurt something.
I refuse to believe anyone will be assigned to Atlantis without knowing or being tested what ATA gene is, or not knowing what the cloak is several days after being in the city, considering that the city itself is cloaked at the time.
Atlantis is remaining on Earth, fine, sure, whatever. But they are closing it down, dismantling it, even? Shouldn't it effectively take over the SGC since the Pegasus gates have a priority?
"Air force has taken control of Atlantis" - what else is new? I mean, when wasn't it effectively under the control of the air force? I suppose there was IOA oversight, and two Atlantis leaders were technically civilians, but Carter wasn't, and John himself isn't, so why do they treat Jack like he is the devil incarnate? How is that different from before?
Poor pacing - if you open up in between Pegasus an the Milky Way, but then spend half the book flashing back to the time you weren't sure if you would be able to fly back, well, that shoots that conflict out of the water. And, it stays like that throughout the rest of the book - the characters move locales at least twice a chapter, they introduce points of conflict (sometimes resurrecting the points of conflict that have long since resolved) only to immediately discard them barely a chapter later. They introduce characters about whom I know nothing and care even less, only to immediately make their presence irrelevant.
Queen Death and everything she represents makes me want to facepalm. The authors wanted to make the wraith behave as humans as much as possible, starting from giving them names that are somehow in public use among humans (since when? I get some need to point who is talking to whom in a written medium, but the series itself always managed just fine, and even if I could accept that wraith might have their own names, they have never bothered giving them to humans even when politely asked). And a name like "Queen Death" is certainly very reminiscent of baby's first OC. Hi my name is Ebony Dark'ness Dementia Raven Way. Not to mention her actions are stupid, the way the wraith interactions are portrayed are nonsensical, and while I am at it, the human politics as they were portrayed were are just as cringeworthy.
I could certainly go on.