Bookshelf speakers are generally more aesthetically pleasing. The drivers are also often of a higher quality in a given price range because you don't need an amp section, or active crossovers, which can be quite pricy. For example the Dynaudio passive speaker line by Dynaudio's own admission have much higher quality drivers than their active line, but their active line gets better performance out of their parts due to the superior qualities of active crossovers and DSP. For example even their Dynaudio AIR series of active speakers ($5000 price range) they use the drivers that are from the lower levels of their passive line, the DM and Focal series, whereas their Contour and Confidence series, which are closer in price to their flagship Actives, have superior drivers, but use less effective passive crossovers.
The best of both worlds would be passive speakers in the hands of a good DIYer who knows how to design crossover slopes, and a high end active crossover unit like DEQX.