Keep the same 18MP, but make the DR better and improve both the low end noise as well as the high end noise.
For me personally a clean ISO 1600 would be perfect, comparable to the ISO 400 of the 40D.
The AF is working just fine for me! I recently picked up a 7D after coming from a 40D. The rumors that the 7D was not to be upgraded, and the price of the 5DIII, made me go for it. If a new 7D comes out, I will buy it in a heartbeat.