Anecdotally, the most derogatory comments in this thread were almost invariable directed against either the female characters or Magus. Quite fascinating.
Could it actually be that Compendium members have something against long hair? The "which Chrono character would you date?" thread has Lucca in top place, showing that there's quite a bit of respect for women with brains. Either that, or there's a lot of fetishizing of brainiacs. Whichever of those two is most likely to be invoked in a dating poll I guess.
Separating this poll from the rest of your observations for a moment, would there not also be a subtle sexism in holding back criticism of female characters, essentially giving them a privileged "pass" precisely because they're female? So long as the character was booted for real character flaws and her gender didn't factor into the decision, I wouldn't consider it sexist.
On the contrary, I'd propose that if the female Chrono Trigger characters are perceived as being more flawed than the male characters in general, this may be a reflection of sexism on the part of the scenario writers and not the fans. As a hypothetical example, suppose the writers imbued Marle with misconceived notions of femininity, making her screamy, physically weak and a healer (...oh), so that she could contrast a muscle-bound, silent love interest capable of immense destruction. Players might dislike Marle precisely because they, having been raised in an environment shaped by the feminist movement, think Marle is a poor role model for women.
That example aside, I do think the CT developers did fair job writing the women given the production team's technical and design restrictions. Lucca was especially fantastic. My only complaint would be that Ayla is oversexualized; but even then, her strength made the player respect her, and she displays pretty deep wisdom given her origins.