I think I may know where you are coming from. I was extremely self-conscious that my female characters were shallow or that I was missing some point of view that would make them believable. An even worse fear was that I was presenting them in a chauvinistic and offensive manner. To work through this, I would enlist women who were friends of mine to critique the portrayals. After a few of these review sessions, I got a feel as to how to properly research and flesh out the female protagonists/antagonists well enough that they became just another character to invent through the writing process.
To the fool, he who speaks wisdom will sound foolish.
I think, for me at least, it's possibly easier to write about a strong female lead than a male one. As I'm a guy in real life, I tend to miss some of the key things that others might want to read about in a male protagonist. When I have to write from the female perspective, it makes me think a lot more about how they should be, what they should do, and all of that. It's a lot easier for me to get into the character in a good way, because there's so many more details I have to think about and make work. I don't know if that makes much sense, but that's how it seems to be for me.
When I write male characters, it seems more difficult sometimes because I forget to add certain things or just ignore parts that I tend to think of as matter-of-fact since I might take the situation/thing/whatever for granted as I deal with that kind of stuff daily. I much prefer writing female characters for this reason because it's just something entirely different from my everyday life and I find that interesting in its own way.
Might be helpful to study the lives of modern women athletes. The locker room culture that develops around professional athletes is startlingly similar to the military culture (with some obvious differences, lol). Read a biography on some female from an athletics team will probably help you pick out details of character that will stand out as contrary to the overall perception... and flesh out the character.
One pro writer I know recommends reading romance novels. He says that if you want to understand women, read the stuff they read. I'm pretty sure he means the high-end well-recommended ones. Studying Barbara Cartland will just give you a speech impediment.
I was at a reception at a conference my wife was attending and while looking around the room noticed a young woman. She was wearing a button-down shirt and slacks that had a masculine cut to them. They were fitted and very flattering to her figure, but the tailoring was nevertheless very masculine. She had broad shoulders and thin hips--the body type you would usually see on an active swimmer. Her short blonde hair was pulled back in a simple pony-tail, and her face had only the barest touch of make-up. She was standing with a hand on her hip which was jutting out sharply to the right. Her stance was wide. She was a strange combination of masculine and feminine.
When writing a female character in a recent story, I thought back to this woman and the impression she had made on me from across the room. I needed a strong character, so I started by giving her a strong presence. What she said and what she did was almost secondary to who she was. And what she was started with how she presented herself to the world.
Hope that helps.
Not really the point of his post, but archguyscifi touches on an interesting point: Its not all that hard to characterize a woman from a Male POV. The challenge is writing a woman from a woman's PoV and being male. That tends to be where my wife throws her hands up and says a character is obviously written by a male
Wide shoulders, narrow hips, masculine body language? My first thought would have been to wonder whether she's transgendered.
Or a victim of bovine growth hormone.