If you are one that likes long rides and doesn't intend on racing the thing, I can very heartily recommend a Cannondale Synapse. (Not that you can't race it, it'd be fine to race, but that's more a six13's job)
It's so amazingly comfortable, not in a "feels like suspension" sense, but more a "hey I've been riding this thing for 5 hours and it only feels like 1" way. (At least the carbon ones are like that, I haven't ridden an Alu Synapse to compare.) I thought I had my old CAAD5 (an older-but-still-recent Cannondale aluminium frame) bike dialed in comfort wise, I took a test ride of a Synapse prototype that wasn't even in my size and was blown away by how comfortable it was. The one I bought (ordered about 30 seconds after returning to the bike shop no less) is actually fit to me, and even better
The frameset is also very light, I think it's pretty much on par with the six13 weight-wise.
Climbing/sprinting wise the initial acceleration doesn't feel quite as instant as the CAAD5, but it's in no way flexy power transmission wise. It's probably just as good, but feels a bit muted because of the way the frame is designed.
To add to what Jaguar says re: keeping tyre pressures constant to eliminate other factors, also ride bikes using the same wheelset if you can -- stiff wheelsets can make the ride feel more jarring.
Compact cranks make good sense. If you think gearing may be an issue (or if you like the idea of having some easy gears in case you're on the tail end of a long ride and just don't want to work hard to get home) I'd lean more towards getting a compact crank from the start, rather than putting on a wide-ratio cassette; that way your gearing is still quite tightly spaced and you still have low gears.
And just to fool you into thinking I'm not a raving ultra-biased Cannondale fan (hehe): if the comfort-factor sounds appealing, you might also want to check out the Specialized Roubaix. It's another bike designed for that "performance century rider" type of riding. I've also heard LOOK frames are very nice comfort-performance wise.