It's a hell of a risk to take though, getting off the ferry at Wadi Halfa, being impounded and then having to take the ferry back the other way and then having to reimport into Egypt. I might be more inclined to risk it once the road is open but even ... Some friends were held for hours at Sudan immigration with a suspected Israeli stamp in their passport (it was actually ethiopian) and they weren't very friendly about it.
Most people do report that getting the Sudanese visa is much easier in Aswan. When I was last in Cairo (last September) the Sudanese embassy was giving overlanders a hard time claiming it would take three weeks to process their applications (possibly less if they paid extra). All three sets of travelers this happened to whilst I was there went on to get their visas in Aswan with no problem.
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