Yes, I've noticed that too, but it seems to be a bigger issue with female characters, since the majority of them wear very short skirts. The male characters tend to wear at least knee-length shorts, if not full-leg-length pants. In addition, some of these male characters, such as Vaan and Jecht, are also shirtless, and to show off the full torso, they would have to wear low-rise pants/shorts as well. Female characters, however, tend to wear very short mini-skirts that only barely keep their hips covered (not to mention that it also exposes their panties underneath). Furthermore, keep in mind that some of these female characters, such as Tifa (in both her default VII attire and her Crisis Core attire) and Rikku (in her X-2 attire) also do away with shirts, and only wear bras as their only clothing to cover up their breasts, since bare female breasts are not allowed (no such taboo applies to the male chest, though).
Personally, like you said, I also don't mind male characters (or female characters) wearing low-rise jeans or other pants, as long as their cracks and underwears are covered. And I also don't like baggy, saggy pants, either.
As for the belts and zippers, well, I've noticed that Tetsuya Nomura has toned those features down as well, but it still pops up from time to time.