Assuming that all else is equal (all components, wheels, tires, etc. are the same), which would you consider a better bike/frame? In carbon, the Cervelo R3 or Ridley Fenix?
I know it may not be the kind of thing that is easy to compare, but in terms of speed/efficiency, comfort, and endurance over long rides, which would you choose?

Both are good. The only thing I can say is there are many more published reviews on the Cervelo. I can't remember anything negative and the reviews are very positive on the Cervelo. For some reason magazines and web sources haven't said much about Ridley.

Lots of R3's out there. I love my Ridley. Be different. In reality it's the rider not the bike.

I doubt you are going to get meaningful answers as both a bit less common. I am just in process of getting an R3 Ultegra, so I know that one, Ridley not sold in my town. From what I can see the regular Fenix carbon doesn't come specced as high s the R3, but the Fenix SL does. I think you'd need to compare the geometries carefully to see if similar (I think so from a quick look). They both seem very similar in "type"- high end 'endurance' oriented race bikes. My guess (and apologies in advance if I'm wrong) is that if someone isn't paying you to ride one of these, they are both vastly more capable than you are - sure is true for me at least. Sastre won 2008 Tour de France on an R3 and I think both bikes have won or placed high in spring classics. I'd say whichever is better deal, appeals to you aesthetically, or you like the shop.

I checked the latest Velonews Buyers Guide. They rate the Fenix SL very high. It's in the Endurance category and what's interesting is the Cervelo C5 is in the same group. I guess the Cervelo R3 is the race category Cervelo although it has a taller head tube than most race style.