Peronally, it truly is a FLAWLESS game.
The plot was quite thick for the SNES RPG era (and still stands as one of the best, most original video game plots EVER). It was also comfortably paced, with the length making it not too long, but not too short.
The only 'flaws' (and they aren't even real flaws, just two things I figured could've been built upon) were:
1.) All the time-traveling could've made more of an impact, with the overall plot having had more explanations for events and what not. The game could've spoon fed us some more (instead of us all conversing and making our own canonical ideas). Then again, that's actually a reason a like it, so this is a matter of preference.
2.) I would've liked to have seen more character development. For instance, here are several idea's:
<Crono - Maybe has problems with his childhood and the absense of his father (perhaps he died, perhaps imprisoned, maybe even just disappeared, etc.)
<Marle - I felt she had the most development, and for her I have no real complaints. She had family issues with her father and with her mother's death, and she was quite rebellious. This was pretty much solved in the game as she grew as a character.
<Lucca - She was a genious, and the only real development we got was that her mother's legs had been ravaged by a malfunctioning machine. It is assumed that this was the reason Lucca became so interested in machinery, because she was incapable of saving her mother. Then again, maybe she just inherited her father's love of tinkering with machinery.
<Ayla - Little development, mainly just Humans -vs- the Reptites. Maybe she could've struggled with defining 'humanity' or the differences in Humans and Reptites. I dunno, something. Maybe even some development between her and Kino...?
<Frog - I always thought that he would've made a great character to base around chivalry and religion. He struggled with self-guilt and lacking faith in oneself, but it would've been nice to see him as relgious and revrent. Not necessarily a zealot (and his religious doesn't have to be Christianity - it could've been left open-ended), but a follower. For instance, maybe he didn't want to hurt others because of religious reasons but comes to grip with fighting as a means of protecting his religious and his friends. I dunno. He could've also been instilled with a stronger sense of chivalry.
<Robo - A great internal struggle would've been nice: "am I man or machine?" Although he was a machine, his loyalties could have posed a problem for him. He was a literal machine but had the mind and self-awareness of seemingly human. He could have dealt with struggling to find loyalties. Or something along those lines.
<Magus - The character was great. I would've liked to see him just fleshed out more...to make him more of a tragic hero. Magus has such a great story, a little bit of filler would'nt hurt, however.
I hope this helped...?
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