Of the 4 choices given, i would have to say plot holes, there were too many, and "The Entity did it" is a really bad explanation
aside from that, i really wish it hadn't been left to the PSX version and CC to figure out what happened to the main characters. You don't know about Crono, Marle, and Lucca being dead until you see the ending cutscene for the PSX version and then play through the beginning of CC to find out that Lynx killed Lucca. Frog's story is wrapped up, but other than that, Schala, Magus, Robo, and Ayla are pretty much all ignored when loose ends are tied up. Schala's story is finished only in CC, and Magus (most important character plotwise IMO) is completely ignored, because SE didn't feel like spending the time to give him a proper storytelling as Magil in CC.
short answer, the biggest flaw is that SE got lazy.
- Anti