A simple 2-way with really good drivers and crossover put in a properly designed box can be absolutely stellar. As stanwal menionted, you're most likely to give up deep bass from a good 2-way, because anything larger than an 8" woofer tends to cause other issues. Bass output is relative to the room, and can always be augmented by a subwoofer (or two).
A 2-way is simpler to design, and less costly to buy good parts for, so when shopping at a price point that's worth keeping in mind, but it really depends on what you're preferences are and what the specific speakers are. I'd personally rather buy a well made smaller 2-way to get stellar mids and highs, then add a sub if necessary, than to give up that critical clarity permanently just so I get more bass output from a larger 3-way. Just my preference.