Females Are More Innocent

While most antagonists are male and/or genderless, in some games, some are not. And similar to animes, other games and/or TV shows, there are enemies of almost any kind. Sometimes, whenever a female antagonist is present (if it's not The Baroness), chances are she might be not particularly evil.
4 vs. Satan:
*The six Helpers are gender-equal and except their leader and some cruelty aside, they're partly doing everything to survive Satan's terror reign.
Alex in Princess Quest:
*N/A
The Stone of Power:
*Artimus' family and followers hardly qualify as villains given Artimus' sympathic reasons. Some could claim the king of the east kingdom and Balthar are the only true villains in the game.
The Three Kingdoms
*N/A
Dragondawn
*Averted. The game has no female antagonists.
Harter Knall
*The S6-unit are also gender-equal. And they're helping the tyrannic king simply because they tried in once and failed and have no choice, but to help them.
Hero Story
*N/A
Kill the Demons
*Averted. The game has no female antagonists.
Satan Saga
*Zig-zagged. On one hand, Millie and Xalia are not as much evil as their allies (the former wanted to avenge her mother, their latter had nothing to do with the massacres. On the other hand, the former has no problem in hiring two mass-murderers and we also get Esrah who's just as bad as her boss Satan.
Story of Hero:
*As noted, other than the cult leader Elizon Tataros, most of his allies could be forgiven for their actions given it's just what he ordered them to do, unlike him.
The Legend of Devils
*Esrah didn't really want to help Satan, but the possibility to change happened just too late for her.
The Sidestory Duology:
*Averted. Demonica is just as bad as her male allies and everyone else is male.
The Time Of Bloody Fear:
*Downplayed. While Reika and Feeza are remorseless killers, they still care for each other and the former only wanted her boss's approval. Meanwhile Maltros and Rosh only show care to their minions/allies when they're useful, while the latter only cares about his boss for fanatical reasons.