Chris has already commented on the first issue of Joss Whedon and John Cassaday's Astonishing X-Men, expressing a mild disappointment that pretty well matched my own. The second issue has substantially improved upon its predecessor - mostly by being what should have been the first issue's ending.
The fight against "Ord of the Breakworld" was exactly the sort of by-the-numbers routine that an accomplished Bronze Age writer would've used to spice up an otherwise talky script. (Tim O'Neil discusses this very practice, and its importance in creating a sense of rapidity and plot accomplishment, in his Chuck Austen piece over at The Hurting.) The debut issue would have been much more viscerally satisfying, if not any more original, had it ended around page eleven or twelve of its successor. Its aimless chatter desperately needed the action, while this fight isn't interesting enough to carry an issue on its own.
Ord reads, thus far, like one of the less interesting Buffy villains, somebody whose character isn't defined much beyond that series' vacant and cloying "Big Bad" appelation. His Badness seems to stem from writer fiat - which is where any character trait or plot development comes from, ultimately, but in this case his ability to bounce around the X-Men seems unearned and a little too convenient. That he's finally driven off by the timely arrival of Lockheed the Dragon - an arrival that makes no sense, by the way, if the fight is cut off from Kitty's comments about Lockheed in the last issue, another sign this battle should have happened 11 pages earlier and decompression be damned - is just embarrassing, first to the X-Men and then to any readers who don't idealize the early 80s.
The issue picks up considerably in its second half, after the fight is done and the plot shifts to Whedon's soap-operatic strengths. The Kitty/Emma scene plays well, as Kitty very reasonably reminds us that Emma is the first super-villain, the first face of evil she ever met; I gather that Whedon is ignoring quite a bit of Emma's development between the classic Claremont and Morrison eras, but since that gap happens to match my own I can't bring myself to mind. The scene does what it's supposed to do, reconciling Morrison's damn-the-torpedoes character development with old Claremont continuity and milking the conflicts wherever they don't line up.
The final scene is either the most cliched or the most interesting yet. After the last issue, I suggested the mutant cure plotline was "a little too transparently part of the old X-Men-as-gay-allegory riff," but even at the time I knew that could be a potential strength as well as a weakness. The important thing to treating the X-Men as an allegory of discrimination is, quite simply, not to play it too allegorically. Morrison's U-Men, for example, were intriguing exactly to the extent that they both fed off the parallel and were able to disavow it - had to disavow it, in fact, since surgery doesn't make the transgendered homosexual in the way it made the U-Men mutants, and since I doubt Morrison wanted to imply that all transgendered people are murderous sociopaths.
A rigidly allegorical reading can open up all sorts of disturbing associations that most X-Men writers presumably wouldn't want to make; using this story as an example, I doubt Joss Whedon wants to imply that homosexuality is a disease or that homosexuals are ticking time bombs who destroy their families when they come out. For that matter, I doubt any X-Men writer would want to carry the allegory to the point of claiming homosexuality is a genetic aberration; at some point the analogy has to break down. However, some bigots of the "gay recovery" movement might make those claims, and that's where Whedon's story about a cure for mutation appears to be heading.
Back to that final scene: Hank McCoy is the perfect choice of X-Man to seek out this cure since, courtesy of Morrison's run, he's already gay-identified but not actually gay. That sexual ambiguity calls our attention to the gay-recovery angle but also leaves Whedon wiggle room to dismiss it or work around it, preventing the allegory from becoming tiresome or downright offensive. That scene and what it implies about Hank are smartly conceived and well-executed; hopefully Astonishing X-Men will continue to improve into more than just another nostalgia exercise.
It's a shame Hank's not gay. He'd be very popular among bears.
It's also worth noting that Hank changed from his original mutant form to the furry one (at first grey, then blue, then leonine as things changed over the years) due to ingesting his discovery of the "chemical cause of mutation". So you gotta figure he'd have an interest in it's opposite number.
That gradual, not entirely voluntary progression of mutations is another reason Hank makes such a good candidate for the cure (assuming his interest is genuine and not just part of some plan to investigate Rao) - it makes sense within continuity and doesn't force Whedon to overplay the allegory.