Looking back on the Xeno games, I'm starting to wonder if the plot dealing with the High Entia and their desire to breed with human may have been a holdover from Xenogears, as I can totally see Kislev's issues with mutants may have developed into a similar situation. It just always seemed to me like Kaiser Sigmund knew more about what may have been going on than he let on. I also bet the Life Recycling Act from Saga may have shades of this as well.

I'm wondering if any unfinished plot points from one game made it into one of Takahashi's later titles?