In terms of sonic quality, nothing beats separates and bi-amplifciation. More complex but the best for many old audio enthusiast i've come across.
Corollary to this is that the simplest approach also has its merits in, for ex: single driver crossover-less speakers often associated with low powered SET amps favored by audio enthusiasts I have come across. Often times, the less components in the audio chain, the less areas for a potential mismatch.
Think of a system that begins with a CD Transport, DAC, Preamp, HF amplifier, LF amplifier, bookshelves and a sub. 4 interconnects, 2 runs of speaker wire and another run to the sub. The implications are evident.
I think that both schools of thought prevail when considering floorstanders and bookshelf+sub combo. Integrating a sub into your 2 channel system is not always a snap. As mentioned, room acoustics can cause certain low octaves to bloat due to frequency overlaps.
Floorstanders, especially true 3-way speakers brings a coherence to it that may not go as deep as standmounts with a sub but also, (brand dependent), can produce a flatter response over a narrower bandwith.