So our "earliest manuscripts", that are complete and clearly ommit them, were written in the fourth century, such as the codices Vaticanus and Sinaiticus. Prior to this, we already have Church Fathers that mention the Pericope Adulterae and the Long Ending of Mark - meaning, when they were copied, these were already extent, and we are merely dealing with variant versions that had both been present at the time.
So why give primacy to the shorter forms? It is merely the luck of history, of which manuscripts happened to survive, that our "earliest manuscripts" ommit them. The actual reason is that Form Criticism decided that shorter forms are more original, based on the premise that the Gospels aren't unitary narratives, but a combination of stories and anecdotes that the early Church wove together. This is, of course, merely assumption that the Gospels don't represent a real linear remembered narrative, and that longer forms must be later as material was added. But people abridge as much as they add, as we can see in Soviet forms of Doestoeyevsky or abridged Shakespeare or such. The grounds are highly equivocal to affirm the short version 'original' therefore.
Further, the short version of Mark seems abrupt and unfinished, not completing the literary themes within the Gospel. Form Critics say this is why it was later extended, but you may as well argue why the work was left so incomplete in the first place? To me, that rather argues for the Long ending.
But what of the Codices themselves? They possibly represent copies prepared for Constantine, which would explain a lot - certainly the omission of the Pericope Adulterae. Constantine had his wife baked to death in a bathhouse for Adultery, and it certainly would be a Biblical rebuke. Augustine in fact mentions copyists purposefully leaving it out, for fear that it somehow gives wives leniency to sleeping around. So it would make sense for one of the Emperor's henchmen, or merely assidious or oleaginous scribes, to ommit the passage in Bibles made for him to assuage the embarrassment.
