It was actually confirmed that Gaspar, the Guru of Time, was going to be a party member, not Schala as was commonly theorized. May also have an (intentional?) Orphaned Reference in the SNES translation: "If you really want to thank me, make me a member of your team!"
Massato Kato stated in his CT Ultimania interview that he and Yuji Horii intended for Crono to stay dead after the Ocean Palace scenario. The party would retrieve a version of him predating the Millennial Fair to complete the quest, and then return him to his home time, bittersweetly knowing he would go on to die at the Ocean Palace. Square deemed this too depressing and had them write the clone plot device to save him.