Hmm I don’t understand either story 100% but from what I think they are about:
-The Zohar and Frozen Flame are both powerful objects beyond human comprehension and both are carried in space at some point
-Miang and Harle, are both female and something something DNA and God
-Grahf and Lynx, both are a percentage of the protagonists’ father and both transform into something else. Grahf/Khan, Lynx/Wazuki... the new forms are not human anymore.
-Alice and Leena- both are female characters that are interested in the protagonist met in the beginning starting village, and both do not end with the main character. Both get neglected really hard in the plot.
-chuchu and Starky- both philosophical mascot goofy little critters from space that can become giants.
-The Elements and 4 Acacia Devas- theres like two generations of them in each game, and there are four of them. First generation of Elements: Jessie, Sigurd, Citan, Ramsus, with a second generation of those Sailor Moon Girls, and then for Cross, we get Viper, Garai, Radius, and Zappa, with a second generation of Karsh, ZOAH, Dario, and Marcy. We also get a Fifth person in the second generation who have potential to be part of them but just aren't (Elly and Glenn).
-Zeboim ruins and Chronopolis- Something something Science gone wrong
-Gazel Ministry and Mother Brain- Super computers... not from the current area, like the Gazel Ministry is up in space while Mother Brain is in the future.
-Both are about the mind, the unconscious in Xenogears and dreams in Chrono Cross
-Both games have cutscenes where the main character gets butt naked!
-Xenogears is a convoluted epic story about a love that transcends time and reincarnated lives, while Chrono Cross is also a convoluted epic story about a love that transcends parallel worlds ..
(-Not really a plot thing, but both games have Chapter titles as well as two other party members following behind)
Idk ill probably add more if I think about it more, and i really want people to clarify and correct me and stuff!