Vena: you flatter me, but to give credit where credit is due I'm 99% sure you were the one who first pointed out that inconsistency ("why hasn't Aquarion gone berserk for Amata and Mikono yet?"), all I can claim credit for is
In terms of generally "what are these writers thinking (about Zessica/Kagura)?", I think what it has to be is that Amata and Mikono are the main characters, but for there to be meaningful issues around the identities of the reincarnations the writers decided there needs one more of each lead (whence Zessica and Kagura)...but for them to believably fit into the reincarnation shenanigans, etc., and to make them plausible they need to be built up into at least "major minor character status". That's all there is too it, I'm thinking. Note this isn't meant to take a stance on the actual reincarnation shenanigans, just that to have them also in the running means committing to a certain level of focus and certain amount of screentime.
In particular, they can't have Zessica exit the stage so soon, because she's working two jobs (romantic foil to the leads, but also involved in the reincarnation shenanigans).