Totally different bikes!
Synapse is a "sportive" bike, more upright and relaxed.
SuperSix is a thoroughbred racer.
I would vote SuperSix because it is easier to modify the fit to raise the front end and shorten reach to emmulate the position of a "sportive" geometry frame on a race bike than it is to lower and extend it to emmulate a race geometry on a sportive frame (based on the most readily available components, if you search enough you can do either), i.e. oddly enough a race geometry is more readily adaptable in terms of fit than a sportive frame. I think the sportive frame may have slacker angles and longer wheelbase too, so it won't be as responsive, but it is a while since I looked at the geometry so not sure on this.
The comfort features such as SAVE seatstays on the Synapse, I am not sure if they carry over to the SuperSix or not, I wouldn't worry about those either way, they won't increase comfort hugely with regards to the Synapse, nor will they add enough flex to warrant concerns of power transfer with regards to the SuperSix (if it has them). My TT bike has SAVE micro suspension seatstays, they claim it makes it more comfortable for a triathlete so they can run better after, but lets face it, a TT bike is hardly built for max comfort, these do not compromise speed to any degree a mortal would notice.