Not sure about the Phages, but I have wondered if he had a different endgame in mind with Nehelenia. Sailor Moon was quite adamant about never losing to her in the SuperS finale, which makes me think he had something other than a redemption arc planned.
Nehelenia in SuperS had an extreme case of Peter Pan syndrome, worse than what the Quartet had (but pretty similar to Akio in Utena.) Lemures being "living corpses because they have no dreams" is probably some kind of social commentary, too. Her redemption arc probably came about because they decided to make her return one big reference to the Snow Queen, which is a pretty different fairy tale than the ones they went off of previously.
But I have no idea if anything in Stars would have been much different at all if Ikuhara stayed. You'd probably need screenwrite Yoji Enokido to stay as well for a serious change. Although simply having Ikuko Itoh stay would have changed the outcome on a visual level for the better~