I have rim brakes on my lightweight bike, prefer the aesthetics and weight advantage that they currently have. On my aero bike, it is disc. I find the disc option more fiddly in terms of keeping it from rubbing - I encountered this first with my MTB - but there is just no denying that disc is ultimately superior at the job of stopping the bike.
In my case, I put Zipp carbon wheels on my light bike and that makes it worse for rim - not a bike I'd ride anymore in anything approaching damp weather. Disc doesn't have that issue, of course. But even rim married to good alu wheels can't quite match disc in the dry, albeit it is closer than some think - disc only really shows a significant advantage in wet conditions.
I guess it also depends upon how fast you ride, heavy you are and therefore how much stopping power you need in any given situation.