gmichael has asked the right question first: what is it about the YPAO settings that you do not like? Were you careful to follow the directions on microphone placement in the manual? You might want to run it again, carefully following the directions, to see if you get a better result.
YPAO usually does a good job of setting distances (aka delays) and levels, but with at least some versions of YPAO, it is not good at picking the size of the speakers (aka bass management crossover frequency to subwoofer). Fortunately, that is easy to do manually in the setup menu. Consult the manual if you have trouble figuring that out (and if you lost your manual, you can download one from Yamaha with free registration with their site).
If you are going to set the levels manually (which I do not recommend), you will need an SPL meter to get it as good as YPAO can do it.
Of course, it may be that you are wanting the levels wrong for some reason, and that means that you will not like the way YPAO does it, as it sets the levels pretty well right.