3-ways, in the past, have generally been the best of both worlds. Great transient response with better low end extension. Two ways were either one, or the other. The 4" mids had great transient response, but poor low end extension. 5.25" were a good compramise between 4", and 6.5". 6.5's usually had good low end extension, but y0u could hear a slight, to very noticeable muddiness to the upper mid frequencies. Some pulled it off...most didn't. MB Quart had done a geat job with their 6.5" two ways. I had stayed with 5.25"...until recently. The Boston Acoustics Pro 60's have done a great job using a neodynium magnet for the woofer! Not just the tweeter. This allows them greater motor magnet strength to help with transient response. I don't want to bore with tons of useless detail. The end result is a two way that works as well as a 3 way, but using less space, and fewer parts.
3-way systems are tough to find proper mounting locations for, anyway. Heck, as far as that goes, I prefer coaxial mounting. BTW, I got me B/A Pro 60's for $265, on line. And, they sound Sweeeet!