The thing is, a lot of S1000RR buyers do consider it a looker, so it's not always a case of simply the spec sheet and hp/$ making it the top seller. Just check out BMW forums or chat up some owners at the local club for evidence of this. I personally know a few blokes who love it.
It's the same deal with the V4, and I dare say the Duc is a mite bit prettier in the overall package. Looks are always subjective after all, and based on what I've seen the ones that absolutely hate it are more of a vocal minority than the norm.
I think maybe some are just bored with red, lol. Agreed on the 1299, it just works for its gorgeous lines, but for most other bikes red is just ubiquitous and perhaps a touch uninspired. Wish there were a couple more official colours for the base and S V4. Maybe that's sacrilege for longtime Ducatisti but I'm fairly new to the brand, that's why I think this thread is absolute gold, though I don't see anything particularly wrong with keeping the V4 plain vanilla red for those that do like it. Just my preference. I see a red bike and I want to paint it black.