The advantage of a typical 3 way is, that it allows you to get 300hz and up at dash level or higher (although you can do the same with a 6.5 and 2.5-3" mid on the dash). All height cue frequencies are dash level or higher. I feel that visually this alignment gives the stage a bit more cohesion, and you tend to notice depth a bit more.
Tonally, there's no difference between a 2 way and a 3 way, as long as drivers are appropriately chosen. If you're tuning to a ref sound, how close you get to it is down to first and foremost your tuning skills, followed by choice of drivers for the application. A 2 way vs 3 way is not part of this equation. It takes more work dialing in a 3 way as already mentioned and if A and B have equal tuning skills, and the driver choice is right, then A's 2 way will be at par tonally with B's 3 way.
