Well, this should make some interesting discussion,
Most monitor companies build 2 way systems due to them not having as many issues as 3 way due to the crossover points, the crossovers themselves and phase issues caused by the multiple speakers. In fact the most accurate system phase wise would be a single speaker monitor (auratone, berritone, etc) but the demands on a singe speaker for larger systems is beyond the frequency range of the singe speaker.
However there is another train of thought that to get a truly accurate reproduction a 3 way system is need to accurately reproduce mids so that the same speaker is not reproducing bass. Most 3 way monitors will be 3 way because the bass driver is large for better bass reproduction and the separate mid speaker is needed because of the bass drivers large size messing up the mids.
In a small room stick with a 2 way, max 6" driver and don't use a sub unless the room acoustics have been worked on, and then only a small sub.
In theory, a 3-way system is potentially a little better than a 2-way. But to do that properly costs a lot more, and 2-way speakers can be very good indeed. Especially self-powered models. So unless you have a lot of money to spend, I'd stick with a good 2-way.
As for a subwoofer, unless you're mixing 5.1 surround music for movies I think you'll do better with good speakers that can get down to at last 50 Hz (or lower). Integrating a sub properly is not simple, because bass frequencies come from three locations instead of only two.