For us what gives the Poly the edge over the CR is the fact that the Poly is an easy walk to the TTC, making the trip to Epcot extremely efficient. In fact, it is so easy that we consider the Poly an MK/Epcot resort!

From the CR, it is necessary to switch monorails at the TTC, which is annoying in our experience. On the other hand, you can walk to the MK from the CR, which you can't do from the Poly, and you have direct access to the MK bus depot, which gets you quickly to any other resort on-property for dining and exploring. Overall, we think the Poly has the best location on-property. Of course, this is subjective.
We also love the tropical theme and the gorgeous grounds at the Poly. The CR is more concrete and buildings to us, while the Poly is pools, palm trees and flowers.
The views from each are very different. CR is close-up castle, Space Mountain and many other attractions. There is also a parking lot in your view. If you're high enough, it's easy to overlook it, but if you are in a relatively low room, it feels like a big portion of your view is parking lot. The Poly is much further away from the park and you can really only see the top of the castle due to many trees in the way (it's much better from the 3rd floor than the 1st). But the foreground is the gorgeous beach, palm trees and lagoon rather than a parking lot.
The Poly rooms were all completely rehabbed in 2005? and the CR was done right after that, I believe. There are rumors that another rehab at the Poly is scheduled to start in the fall, since one is due. The rooms in general at Disney are pretty well-kept, though they do see lots of traffic with families that can cause quite a beating. Disney rooms in general are completely refurbed every 7 years or so, much more frequently than at many other resorts outside WDW. I doubt more than a few rooms are in bad condition, though the one we stayed in in 2010 definitely had a few minor problems. We loved the location and view too much to ask to be moved, but if we had everything broken in our room, we would have asked for a different room.
Honestly, you can't go wrong with any of the monorail resorts. They are all wonderful. Spend time on the FAQ threads for each and go with what speaks to you. There must be a reason why you booked the Poly in the first place?