Seandtaylor99 is right about 2-way design constraint. 3-way or higher do offer drivers to operate in linear region where they are designed for. But like everyone knows, cross over is extremely complicated to design in 2-way already, 3-way is a million times more difficult. In electrical term, we called impedance because it's freq & phase combined.
You will also notice the best speaker on earth usually employee drivers from ONE manufacture. When manufacture design and build drivers, they apply their know-how from one to another and tend to behave similarly in electrical term. So designing a speaker with mulitiple drivers is easier when drivers are from one source.
Among all the speakers I have owned, my all time favorite were Sonus Faber Extrema & Dynaudio Confidence 5. A 2-way & a 3-way. Extrema got everything right, but C5 made everything better. So yes, a well designed 3-way can sound better than 2-way.
If adding a sub solve all the problems, I doubt manufactures can sell those $10k+ speakers as easily as they had. Till this day, I still haven't heard a sub that fully integrated to main speakers seamlessly. My last sub was a REL Stadium III and I ran it very conservatively (in volume) to make integration easier. Even then, I could still hear it from time to time.