The reason that the pins are flat is that ASUS apparently chose not to implement the header for the internal USB 3.0 connector on that motherboard. Most likely they did so to reduce the build cost of the motherboard so that they could offer that one as a budget motherboard. There are also several chips missing from that motherboard(probably the USB 3.0 devices).
I did a comparison on newegg with your board and the next level of the same board and I noticed that one of the differences is that your board does not have any USB 3.0 functionality listed in the features. You can view that here: http://www.newegg.com/Product/Productcompare.aspx?Submit=ENE&N=100007627%2050001315%20600093976%20600158412&IsNodeId=1&bop=And&CompareItemList=280%7C13%2D131%2D773%5E13%2D131%2D773%2DTS%2C13%2D131%2D781%5E13%2D131%2D781%2DTS
If you compare the this one ( http://www.newegg.com/Product/Product.aspx?Item=N82E16813131773
) to yours you will see that it has the connector as well as the additional chips installed on it.
Therefore, your board cannot be made to use USB 3.0 because the chips that are necessary for USB 3.0 are not installed on it.
You have a couple of choices available to you here.
1. return the Motherboard and spend a little more money to get the one that has USB 3.0 functionality installed on it.
2. return the card reader and get one that is compatible with the USB 2.0 headers that you have on your existing motherboard.