Given that most of my business travels send me to places where there are *only* FI's, a couple observations:
1. I also disagree with the poster who said that FI = Super 8, et al. That's generally not true where I stay (outstate MN, SD, IA, ND). The FI is usually one of the better properties in those kinds of places - and they charge accordingly. Fairfield is definitely better than Days Inn, Super 8, etc. in those places. The one location where they have competition in that segment is St. Cloud - the Ramada Limited is just as good, and usually about $20-25/night less.
2. Part of why the Hamptons (I just stayed in one in the LA suburbs) seem better is perhaps because of their new campaign in terms of internal branding. I have to admit it looks pretty slick (i.e., redone signage around for breakfast area, newspaper stand, rooms, etc.). Fairfield hasn't done anything like that in a while, so perhaps it seems a little dated by comparison.
3. I agree with other posters who've noted that there's more variability in terms of FI - that's true. Most of my issues have been noise-related, but then again, I've also had those kinds of issues in full-fledged Hiltons too. What has made the difference, and why I remain loyal to Marriott, is the service at the individual hotels. Despite the variability of the hotel quality, the service has been more consistent at FI/CY. I've been in enough hotels to have had problems at a variety of brands - nothing's perfect - but Marriott seems to take control of the problems with greater frequency than other chains I've dealt with.
Oh, and I'll have to try the renovated CY in Naperville. The last two times I was there was pre-renovation, and was able to get $59/night. That made it an easy call for the CY for me.