First, I would like to briefly acknowledge a couple of distractions before starting to explain what I found missing in After Virtue.
I noticed, especially in the beginning critiques, that the positions MacIntyre critiqued seemed to be always treated as paper-thin concepts, and/or often paper-thin wrappings around emotivism (the doctrine that moral assertions are just statements of our emotions instead of claims about what is right or moral). Meanwhile, his work on his preferred concepts such as a "character" and a "practice" are thick concepts.
Second, I noticed at least one instance of critiquing the concept of the unity of the virtues by positing someone who had the fullness of a virtue and the fullness of a vice. This is begging the question. Elsewhere, in regards to bridging from "is" to "ought," he brings an unacknowledged enthymeme in going from "He is a sea-captain," to "He ought to do the things a sea-captain out to do." The unacknowledged premise is that there are things which a sea-captain ought to do, and MacIntyre on this point fails to provide a legitimate exception to C.S. Lewis's assertion in The Abolition of Man of, "Either the premises concealed an imperative, or the conclusion remains in the indicative." (Aristotelianism does not reach "ought" from "is." Aristotelianism starts with "ought" and builds bridges from some "oughts" to other "oughts." This may be acceptable and in fact I also do so, but what it is not is a bridge from "is" to "ought.") I think that if I had read the text more slowly, I would have detected more fallacies.
I will also mention, not as a critique, that The Benedict Option seems to pick up where After Virtue leaves off, and may be a more interesting followup than MacIntyre's next work, although I am partly guessing because I know only what is implied by his 2nd edition postscripts.
Having briefly mentioned those, I would like to respond to something closer to the substance of the book. MacIntyre works hard to show the failure of all post-medieval Western attempts to build a philosophically justified morality on standard philosophical terms of justification, and I would be inclined to agree with him at least in substance, that for the Western academic conversation, post-medieval Western moral philosophy has failed. No obvious rebuttal to his claims occurs to me now, and his critique, especially for today, only enjoys a sharper edge today for Ian McGilchrist, The Master and His Emissary, where the left-hemispheral monism today cuts off reaching virtue or any truly grounded morality.
But with regard to the rest of the substance of the book I ask, "Why Aristotelianism?" Possibly most or all attempts to produce a grounded morality in the post-medieval West have failed, but why treat Aristotle as the only alternative? Stoicism excluded, he does not give reason why Aristotle is to be preferred over all other ancient and medieval options or options outside of the Western philosophical tradition. Among the Greek Fathers, legitimately calling you an Aristotelian was a strike against you.
I have heard postmodern heterodox make brief formulaic mention of the Church Fathers using "the best available philosophical resources of the day," combined with a complete failure to acknowledge that neo-Platonism was at once the air the Fathers breathed and something they were actively fighting against; an anachronous, if analogous, description might be that the Church Fathers were attempting a critical reception of neo-Platonism. I have never seen this play out in people who use today's slogan attempting to work out of the most fashionable resources of our day. There may be differences in which decisions one makes within a fairly completely assumed postmodern whole, but never a critical reception open to openly rejecting major segments of postmodernism the way Church Fathers repeatedly chastise Plato for mandating that virgins strip for exercise.
G.K. Chesterton said, "The reformer is always right about what is wrong. But he is usually wrong about what is right." Neo-Platonism, which incidentally includes elements of Aristotelianism, is still brought up as a resource for today even in settings not particularly related to Orthodoxy. I would suggest that MacIntyre is right about the failure of all post-Aristotelian Western philosophical attempts he investigates to arrive at a philosophically justified morality, but wrong in basing himself primarily on Aristotelianism from among available premodern philosophical resources. (Although my main interest is not, loosely speaking, critically received neo-Platonism from among the Church Fathers, but patristic Orthodoxy which came before, and survives, the failures in the West that MacIntyre studies.)