No explanation is ever given for why Merlin can't turn Perceval and Tristan back into the forms they had back in the time of the first Camelot. Then it hit me: Merlin's powers are based completely on Satan. He's hit with the Grail in the last issue and it sets off an explosion of some kind. Perceval is one step further than that: he's explicitly a relative of Christ. So Merlin's powers won't work on him, or might even kill him and Merlin both. As for Tristan: he's undergoing karmic retribution from God because he raped a woman in his previous life. Merlin can't go against that because it would be against God's, or fate's, specific will. Merlin's powers are uniformly only useful against those who are evil themselves or "neutral". — Saintheart At Home.
I also asked myself how it was that Arthur got off so lightly when it's (very disturbingly) pointed out he tried to drown Mordred (and succeeded with a number of other babies!) when he was an infant. The punishment for Tristan is apparent: he's made a lesbian. Kay is also dead, a betrayer trying to save Arthur, by the time the revelation comes round. Then it hit me: Arthur has never forgiven himself for what he did. Whilst Kay and Tristan apparently don't remember what they did — Tristan asks himself what he did in his previous life — Arthur does. The next page over, he explains to Tom that the crown has always exacted a heavy price "on those I call my sons", and he embraces Tom as his son. Arthur is undergoing punishment: he is The Chosen One and he can't lay the crown aside; he must always remember and regret his crimes, whilst the others at least are spared that. In addition, Mordred himself is Arthur's punishment. — Saintheart At Home
Regarding Tristan, the punishment isn't that he's reincarnated as a lesbian, it's that he's reincarnated as a woman and thus, to a heterosexual male rapist, would seem like a punishment (just as being turned black would be seen to a white racist). His "punishment" is entirely self-inflicted because of the way he views women. Realizing he can have a relationship with the reincarnated Isolde means he's accepted that a woman is an independent being not dependent a man, even for the most intimate of relationships. In other words; being made a woman was the punishment, his lover being reincarnated as a lesbian was his reward. — Keith M
Why, exactly, was it considered a good idea for Guinevere/Commander Acton to marry Arthur again in this incarnation? It was obvious to everyone that she'd go chasing Lancelot again, and Merlin's claim that their wedding would be a morale-booster for Earth is undermined by the fact that anyone who knew enough about Arthurian legend to care would also know that their last marriage had Gone Horribly Wrong.
Although to be fair the implication is that people don't remember much about Arthurian legend. 'Tis the year 3000, after all, and roughly 900 years or so since World War 3. It's implied all that's widely remembered of the King Arthur legend is that he was the incarnation of Authority Equals Asskicking and that he could pull swords out of stones.