IMO...in the end...when you reach a certain price point (talking retail)...the "quality of the bikes will be similar. It all depends on what you are looking for.
The headtube length to me just seems like nitpicking. You can achieve a lower position by either sizing down or going with a smaller frame. I don't see how running a -17 would be a deal breaker...it wasn't for me.
I also used to work at a shop that sold Cervelos, along with Cannondale and Specialized. I did not wrench...but I do see all the bikes that come in for work. There were no more issues with the Cervelos than there were with the Dales and Specialized. All three use a press fit BB...so that is a wash. For what its worth...I saw more Cannondales come in with creaking BB's than Cervelo and Specialized combined.
The internal routing is kind of a pain...but not as bad as some describe. I routed the cables on my own...and I do minimal wrenching on bikes.
I've had my S2 since late 2011. Its more than enough bike for me. I was thinking about an R3...but since the redesign of the S2/3...I just may end up picking up another S2.