I have an idea in response to the "dark characters" if you're still going to keep them in. Aluding to the split in dimensions in Chrono Cross, maybe the "dark" Crono Marle, Lucca, Janus, and whoever else came from Home World / Another World in an attempt to change the timeline, thereby sending the events of Chrono Cross to the Tesseract. After all, Home world was never meant to take place, supposedly.
Also, it is plausable to have 2 of one character in the same timeline, in at least a different dimensions, as in Chrono Cross. And, backing up the characters coming from the future in the same dimension, in CT in 600 AD, if you do the Shrine Sidequest, you can have Robo on the field fixing up the forest AND have Robo in your party, having 2 Robo's, same dimension, same timeline, in the same place, at the same time.
Ok, I'm babbling, but it could work...