There are tons of very bright women out there who don't need any special treatment to do exceptionally well, and now there are few if any institutional hurdles to success that women face that men don't.
Women, in general, tend to place more emphasis on ‘having a life’ and having a family, and I think that therefore there are less of them willing to put up with the BS and politics that are involved in becoming department chairs etc. This, in my opinion is the biggest reason why there aren't more women in those positions.
I played ball, and had several friends who played in the minors. They were good, and were progressing up the ranks at acceptable speed, but they weren't willing to keep riding buses and living that life indefinitely, with only the possibility that they would ‘make it’. So they went on to other things (happily all have been successful). On the other hand, there are plenty of players in the minors who come from Latin countries who stick with it. For them, the salary they are making, and the lifestyle, is as good or better than what they can generally have in their home countries. They hang in there, and eventually some make it to the majors.
My point is that lots of things in life are a choice, and those choices often relate to how much you are willing to sacrifice, and how long you are willing to make those sacrifices.
I have a problem with people who aren't willing to make the sacrifices necessary to achieve what they want, but try to find other reasons why they don't have what they want, usually involving blaming others (these people tend to be democrats).
And that, in essence, is the whole "equal pay" argument. Women want the "mommy track" and are willing to give up total commitment to their careers so they can be committed to their families. There's nothing wrong with that; in fact it's admirable. But the reason the "glass ceiling" and all this pay disparity exists is precisely because most (not all) women don't want the pressure of a full-time CEO career while also being a mother because they don't want to make the commitment that would entail.
I have nothing against women who want a full-time career. Heck, I'd have nothing against having Sarah Palin as POTUS. But most women want the "mommy track" and put their careers on hold (or cut back responsibility) in order to raise a family so they are naturally passed over when the top positions are being filled because they weren't fully committed or didn't want the added responsibility.
It's when they whine about discrimination but aren't willing to put in the time and commitment that becomes difficult to stomach. If ending discrimination is what they want, then maybe we should do away with FMLA since it discriminates against men.