I voted for the Singing Mountain and Lost Village. My first instinct was to go for 1999 A.D., but I think both Chrono Trigger and the Chrono series benefit from leaving that era unplayable in the first Chrono game. The big draw of 1999 is to see the high technology and get a taste of dramatic premonition, because you as the player know that the world is about to be ruined. However, high technology and a foreknowledging of impending destruction are also the hallmarks of the 12,000 B.C. time period, which I think would be diminished by pulling the same dramatic stunt in another era in the same game. Furthermore, leaving 1999 as an enigma allows the possibility of setting some important action there later on in the series.
Meanwhile, the Singing Mountain and Lost Village might have provided a whole new level of depth to the 65 million B.C. era, and could have changed the character of that part of the game entirely. (We'll assume that this change would have been for the better, although that too is a valid point of debate.) Many people criticize the Prehistoric as being CT's least well-developed era, and while I don't necessarily agree with that, I do think that it was rather disjointed and dramatically loose with respect to itself. It seemed to be more a parade of ideas rather than the tightly-knit story that marked the other time periods. I'd like to have seen greater emphasis on the story of the rising tide of humanity against the Reptite order, and more cohesion amongst Prehistoric story elements in general.