As a medium level Precure fan...assuming the presence of pairing tags, I don't really mind the current setup. Generally, if I was going to filter the material I'd do it by pairing anyway. Assuming we haven't got a lot of non-romance/yuri material (which may or may not be a good thing, I guess? I guess there's the potential to miss out on some general comedy) that should generally be enough to narrow results by series. And I do sort of see Precure as a continuity, in that it'd be good for new fans to become familiar with older series.
On the other hand, the monolithic setup does discourage attempting to work through the entire back catalog. Actually I think this question might be better targeted at new Precure fans, or Precure fans new to the reader. As for myself, by this point I mostly track new releases to the Precure section via the Recently Added listing...