I don't think putting more work into a character can make them Mary Sue. In fact, I think quite an opposite. The more you work on a character, the more their flaws and very human characteristics can come through.

Also, I don't see the difference between working on a character you idenitify with of your gender and one not of your gender.

Also , as an anon said before, you are limited by a original character's personality unless you wish to write occ...

True, but most female characters aren't Mary Sues. Not to mention you can write a canonically male character as if they were born belonging to the other gender and/or sex.