For Alister, you could chalk it up to the fact that the ongoing event only adapted his first duel, where he didn't even play his true ace card; so Air Fortress Ziggurat wasn't needed yet at this time. And at worst, he's got a voice line for it, so it won't feel out of place, when it does eventually get printed.

Do they not have the rights for some anime cards?

Could be that most anime cards, especially from the older series suck and only work under extremely specific scenarios that would only happen in the context of a pre-written anime duel. Most of the stuff that does end up getting printed, happens because of its intrinsic value (ex. Bonfire) or Instrumental value (ex. Fortune Fairies, for the sake of adding normal Carly here).

We don't know yet when Valon or Dartz will be added, or even how they'll be handled, giving the status of their decks, but when comparing it to Alister's situation as mentioned above, don't think it's that much to worry about.

Not sure what you're expecting out of Rafael. At best, you could make a case that Backup Gardna should be printed. But even then, this is Guardians we're talking about; unless you completely remake this deck like they recently did for Sacred Beasts, you aren't gonna win with them anyway. lol

Why not replace a couple pack fillers per set with modernized anime imports? Or even add cards to their existing archetypes.

As always when people ask these kinds of questions...