I believe most of us here have played hundreds of games. With such accumulated experience, let us reference the basics of good game designing (be it the 'do's or the 'don't's).
Article I: Party balancing in regards to gender
The cast of characters is something very prominent within a game. Although the story and setting can modify the common basic rules, one should try and stay as close as possible to them.
When designing the cast, there should be an equal number of men and women (unless as said above the setting does not permit it - ie: a Sailor Moon game). If the game features character classes or types of characters, there should be as much as possible a male and female character for each. This permits the player to create either a mixed gender party or a single gender party while retaining balance.
A common error is to split roles between sex. Many times have games put males into tank/physical damage roles while female were support/magical damage roles.
In reality, either a man or a woman can take about equal amounts of wounds before dying and so a physical female should not be a taboo nor should she be brittle as glass.
Examples of good party balancing:
Star Ocean 3
Although the game has an imbalance between male/female toughness, there is a female and male exception to balance it. An all male or all female party is still very balanced.
3 male tank characters, 1 female tank character
1 male light fighter, 3 female light fighters
1 male mage, 1 female mage
Dragon Age 2
1 hero (variable), 2 rogues (1 male, 1 female), 2 warriors (1 male, 1 female) 2 mages (1 male, 1 female) + extras (1 male sibling, 1 female sibling, 1 DLC male rogue)
Examples of bad party balancing:
Ogre Battle 64
Every male class are tough, mostly tanks or physical damagers. No male healers.
Every female class are fragile, mostly mages or supports. Not a single good front row class.
Valkyrie Profile 2
Every heavy warrior male, every light warrior female, every mage male, every archer (but one, but he uses a modified female model =/) female