There is no secret formula to writing a best selling novel, except to write a good manuscript. If your MC is realistic and strong and well written then your audience will empathize, sympathize, and follow them where ever their travels take them. They will enjoy the adventures of your MC if your MC is likable, sort of everyman and individual, unique and a good friend and perhaps even a hero to some extent. Lovable or funny but definitely someone the reader can associate with. The tales you weave around them will make them popular.
If you believe that only Male MC's stick out in your particular genre then contemplate it for your next manuscript, but in the meantime finish this one as is. Remember that Harry isn't the first wizard student but something about the series helped it take off, Spiderwick isn't the first of its kind and yet something about it appealed in a major way. Perhaps because you have a female in a male dominated sub-genre of fantasy, she will have a following no one anticipated. Either way don't you want to be that unique force? I know I'd want to.
Published Author of Contemporary Interracial Romance