Very few of us are equally good in hard- and software, the issue is not whether you are excellent in either, but whether you are very good at the one you are weakest in. The issue with CS graduates and embedded engineering is that those that not have taken upon themselves to understand what is going on on the other side of the fence (as evidently J. Guy has) are worthless in embedded engineering. An EE degree is more likely to create the basis for understanding software than a CS degree is for understanding hardware. That said I will not outright reject a CS applicant, the trick is to test the CS in hardware and the EE in software.

Have fun,

Erik