The truth of the matter is no one really knows. We on FT have not (yet) gotten access to the algorithmn use to asssign FC upgrade seats. Some feel that CO severly limits "R" inventory so no matter what fare basis you are on, if there are no "R" sets, you can't be upgraded. Others (like me) feel that there are other things at play. I think that on the 5 day and 3 day (at least) EUA runs, CO severely limits any upgrades from any but high yield fares. What is high yield? YHK???? No one really knows. In truth, I think, it is probably some combination of both and for certain city pairs (EWR-IAH, EWR-transcons, etc) it is probably more complicated still.
The only thing sure is that whatever is going on, upgrades are down, and down substantially.