These were the bad guys from my two favorite cartoons I watched as a kid. When you compare thme, which group of villians is more intresting.
I'm going to go with Cobra. Cobra Commander simply looks cooler than Megatron and Destro was actually competent compared to Starscream. Also Cobra had alot of intresting vehicles such as the Hiss tank, and BATT robot's and the Terror Dome, which sort of balanced out the fact that the Decepticon's could transform into vehicles. Cobra also had alot of cool headquarter's and the Decepticon's never did. The autobot's at least had the ark but it seems like the Deception's were always hanging out in rock quaries(wrong spelling).
As for the comic books I also felt the GiJoe comic gave Cobra villians more depth. We sort of got to understand who Cobra Commander was and Destro and I loved things like the civil war they had and it was fun seeing them sort of ground them to more real world motives(at least in the early issue's).