There are several factors entering the picture. Apparently the retina displays use lower power semiconductors, which would explain why Apple gets away with retina displays on iPhones.

It's also worth considering that more pixels means that the CPU and the GPU have to do move more data around the system. The CPU and GPU will also have to do more number crunching in the case of rendered or compressed graphics. Thus more power is consumed there.

There may also be factors related to the LCD itself. I don't know enough about the technology to be sure. Yet higher pixel counts will mean more transistors (assuming it's based on the same technology). Depending upon how the power consumption per transistor relates to pixel density, there could be an increase in power consumption here. There are also other design considerations that may create an impact.

While it is probably that a smaller retina display will use significantly less power than a large retina display, it is unlikely that it uses less power than lower density displays of the same size. And that is what matters. The smaller case of the mini means not just a smaller display that uses less power than it's larger counterpart, but it means less volume to store the battery in. There are also complicating issues on this front. One is that the PCB probably won't shrink as much as the screen/case does (i.e. it probably uses more space proportionally if you want to maintain features and performance). The volume of the case also shrank more rapidly than the size of the screen, since the iPad mini is thinner than the iPad.