I agree that PR value has diminished a lot however it could be a good metric to follow if made appropriately. Even if you got millions of pages, you'll have greater hubs which condense the most value of your site. I'll try to see if all the pages which are 1 or 2 clicks away from your homepage has PR. Low value website are not website with a low value of homepage PR but are sites which has a lot of NaN PR, which google doesn't even bother to evaluate. Be sure that your category pages has at least more than PR1;2 and keep track of pages with NaN or even PR0.
About rankings tracking I think that even low volume keywords can be helpful to see if your site has been reduced its search visibility, I normally keep track of thousands of keywords, so if I see a drop of many even small keywords I can prevent a drop of more improtant ones.