I have an R3 and a 2008 Madone 5.2 (same frame as 5.5). No direct experience with scott. The R3 has a shorter head tube = more saddle/bar drop, which for me as a longer torsoed, short legged, unflexible guy, meant a stack of spacers that looked goofy. The longer head tube of the 5.2 (NOT the Pro fit, but rather the plain 5.2) worked better. If you're a generously stomached build, the longer head tube is most likely a better fit for you, which takes the R3 off your list and puts your decision to the 5.5 or RS (or Scott, which I cant discuss due to absence of knowledge).
I moved components from the R3 to the 5.2 aside from stem and crank set/bb, so I think my comparisons are as apples to apples as one can get. I've raced on both and ridden both +/- 10 K miles.
The handling between the 2 is not differentiable, I think the R3 was a little more plush, but not enough to matter. They both weigh around 15.5 lbs., a little less with race wheels. I bought them both from the same shop, and my own experience is that Trek is a more resonsive company in the customer service area, I found Cervelo to be very difficult to deal with (although the shop had some culpability), and the R3is a more fragile frame - thin top tube is very prone to cracking upon minimal impact.
My recommendation, get the Trek. 100x/100. It'll fit you better than an R3, and IME Trek is a much better company at resolving issues than is Cervelo.
Oh yeah, test rides are IME useless unless you're putting exact same everything on each frame. Get the fitting, that'll point you toward the frame that'll fit you better ... and the bontrager wheels are good, serviceable, durable wheels that you dont really need to upgrade unless you dont like the way they look.
Enjoy, those are all nice machines.