I said that it's too short, as I never like games to end (especially Chrono Trigger since I loved it so much), but in reality I don't know if there are any major flaws. If I had to choose one thing, I'd say that some of the characters could have been developed more (primarily Ayla and Robo, as others have said), which would likely come with a longer game. That and I would have loved to have more quests/sideplots in the Dark Ages before Zeal was destroyed, simply because I absolutely loved the Kingdom of Zeal.