I have no personal experience with using the Anaconda R and RStudio distribution, but I can offer as anecdata some reports of at least one serious problem with anaconda-installed RStudio IDE that have cropped up here. It’s totally murky to me what the source of this problem was (and maybe it wouldn’t have occurred in an IT-managed environment), but it seemed to resolve when people re-installed directly from RStudio-provided downloads.
Also, in at least one instance RStudio folks have remarked here that they don’t support Anaconda installations of the IDE, so I guess you’d be more-on-your-own-than-usual?: