The YPAO will give you a great starting point, but, yeah, it's far from perfect.
I have run it a couple of times, and always end up retreating to manual settings after being unsatisfied with the result. This is not to say that the YPAO doesn't set my system up so that everything is even and balanced, etc., I just like it a bits more when my surrounds are a little "livelier" (louder) and my center is a little livelier. Also, it tends to turn the sub way down on me.
The 2500, I should note, is very different from my 750, from a YPAO standpoint, as the 750 doesn't do any frequency re-eq'ing. From what I understand, this re-equalization can at times destroy the great "axiom" sound, thereby nullifying all that work that Ian and Allen and others have put into this. The equalization is best for cheaper or imbalanced systems - not a system specifically designed to have a particular response across the frequency band and match one another left to right, front to back.
The 750 doesn't do any re-equing, so it is mostly phase and volume adjustments, which might be why I find it very tolerable (and a reasonable alternative to an SPL meter...)
