Well to put it simply its the sound, as well as the simplicity. Some 2 ways may have gaps in the frequency response but are pretty easy to install. 3 way setups are easier to play the full bandwidth but its an extra speaker to find a good place to put.
A speaker can only play so many octaves, no speaker can cleanly play every frequency at the same and level. Breaking the bandwidth up makes it so each speaker can contribute its best part. Thats why subs play low and tweets lay high, they can't do anything else very well.