I have come from a Domane 2014 6 Series Project One (600/700 Carbon mix) , and to be honest, the biggest factor is cadence.
If you like to spin, at >90rpm, you need to look away from the Domane. You will bob, unless you set the seat slider to the hardest setting. So then the Emonda has the same amount of seat tube flex as the current SLR Domane in that setting. I have found I can drive the flats and climb far better on this than I ever could on the Domane. While the comfort of the Domane was superb, the 31mm wide GP4K “28’s” have made this bike a far better proposition. That is, unless you want the front isozone (I never had this on mine). If you want ultimate comfort, get the Domane. If you have even a slight desire to work in the hills or drive hard, get the Emonda. I have massive spinal and shoulder injuries and the Emonda works for me just as well as my old Domane.
I didn't notice any bob in the Domane SLR during my test rides. Maybe I'm not heavy enough? I'm 185 lbs, btw. What I did notice on test rides switching between the Domane SLR and Emonda SL is that the Emonda has a noticeably stiffer bottom bracket. The power transfer to the rear wheel was delightfully "snappy" and direct. But the bottom bracket of the Domane SLR is still stiffer than the old USPS 5500 that i'm upgrading from. I view the Emonda as the direct descendant of that bike (same race geometry), only Trek has upgraded everything in a big way. It's significantly stiffer and lighter at the same time, with that fantastic power transfer. The seat mast even has some noticeable compliance that makes for a more comfortable ride, whereas mine is spine-jarringly solid. And the room for wider tires is icing on the cake. Trek just nailed it.
I'm still up in the air about the direction I want to take. The idea of an endurance bike like the Domane SLR does have it's appeal for me, but the draw of that pure-lightweight-race-bike that is the Emonda is strong. It's a good thing the Madone isn't offered in a disc version yet, or I'd have a real "tri-lemma" on my hands. LOL!