3.5 rounded up this time despite some typos, because not only was the writing very good otherwise, and the characterization excellent, there were so many brilliant thoughts here about all the stuff the Atlantis expedition could have and should have done to be better prepared before making that big 'Gate jump.
Also, did you recognize who the cover art is depicting on the left? This fic is a crossover, and he would have made an amazing Chief Medical Officer, particularly compared to the long research-focused and militarily utterly inexperienced Beckett.
Which brings up a point I should mention: this fic has a Beckett-bashing and especially Weir-bashing perspective, though not carried beyond the bounds of canon-character credibility.
The other crossover element is a couple characters from The Losers, which I'm not familiar with, but they don't play a big role; it's more about establishing the multi-skilled types Sheppard would choose/ suggest/ recruit to go if he could, given the ability to act on hindsight.
Speaking of who should have gone, this fic addresses the lack of support staff (for cooking, cleaning, admin stuff). The featured capable and common-sense leader of those new expedition members is an OC, Cooper, already popular with followers of this author, from a series of shorts with her PoV in a less-AU version of Atlantis.
Another pleasing thing here is the amicable working relationship Sheppard manages to build with Sumner. It'd be interesting to see how things played out in Pegasus with both of them, if John succeeded in keeping him alive, but the fic ends at the "beginning". It's not a cliffhanger or anything, I just wish she'd written the contemplated sequel. (She didn't, AFAICT.)
There is sexual content here, though it's not a major percentage of the fic. Sheppard and McKay have only each other to be fully honest with in this scenario, and attraction unacknowledged in the original timeline is hard to ignore. In terms of plausibility again, I do believe that, as posited, homophobia as well as xenophobia would be important to weed out in any long-term-isolated group trying to make allies, not enemies, with a wide variety of completely foreign cultures, and no part of the Stargate program would be served by enforcing DADT violations.
Anyway, to finish up, I quite liked this story. It doesn't require literal explosions to have gripping moments, many here being in the vein of "How can they stop Weir from carrying through with another blindered, ignorant, naïve, and/or ego-driven idea of what 'her' mission will and will not need to stay alive in Pegasus?"