It's like asking what's better, an apple or an orange. Depends on your taste and in this case what type of riding you are going to be doing. Harley's are built for touring. They have great resale value and can easily be customized. Ducati's are built for the race track.
Personally, I prefer BMW bikes. I admit, they don't look as cool as HD or Ducatis, but they combine reliability, performance and comfort better than any other brand. Resale is strong, but not as good as HD.