The only games I had where you play females are The Little Mermaid, Super Mario Brothers 2, and Micky Mousecapade. Though it's obvious Mickey is the main character, you control Minnie at the same time. She always dies first, and you can never lose Mickey to control only her. The one N/A game we had was Battletank, as it's never indicated if you are a he or she inside the tank. Most all Nintendo games I had growing had were only male characters you controled. I remember being excited to play The Little Mermaid just because we didn't have a game under the sea (except for a level in Battletoads). Kirby (In Kirby's Adventure) I never made in my head as male or female; it was only much later when I heard him referred to as a he that I must have just accepted it. So, not much variety, but then the Super Nintendo came along.
Megaman X2 is included in the 'male' category because he is referred to as a he and looks like a male (and Kirby, while androgynous, is identified as a 'he'--Kirby Super Star). RPG's such as Super Mario RPG, Chrono Trigger, & Earthbound have a playable female character, so they also get 1 entry in each category. The first Mortal Kombat, despite having only 1 female player, still gets an entry in both, as does Super Mario Kart (Princess Toadstool). Shadowrunner is male only; you can hire female bodyguards, but you do not control them. I did not include the compilation game Super Mario All-Stars, as it's not technically a Super Nintendo game.
I've only bought about 8 Super Nintendo since graduating high school that I did not included in the results, and that was pretty much half and half in terms of playable characters: Kendo Rage / Alladin / Mickey Mouse are female / male / male; while Revolution X and SeaQuest are Unknown genders.
I don't even need to tally it. All my games were Bubble Bobble, Star Trek, Legend of Zelda: Link's Awakening, Super Mario Land 1 & 2, Donkey Kong, FIFA '96, Pokemon Red, & TMNT 2: Back From The Sewers (all males). Only Battle Arena Toshinden had a playable female in it (a fighting game). Tetris is obviously N/A.
So, yeah, just something I thought would be interesting to look at. Growing up, I see that the Super Nintendo games we had had a ton of more playable female characters than our original Nintendo ones. Remember, this is only my games growing up, and won't match yours, or the library of either system.