I was running the Continental Grand Prix 4000 s on bontrager rims prior to this upgrade. The contis are great tires! Hutchinson is basically the only tubeless tire provider as of now. That will certainly change in the future. They have 3 tire options. The Atom which is a light weight slick, more of a performance race tire. The fusion 2 and now 3 which is a more durable slick and then the Intensive which is an all purpose trainer tire. Thats the tire I went with. I think the Atom and Fusion are in 23C size. The Intensive is a 25. I am very pleased with the road feel of the Hutchinson tire. I have only been out on the wheelset once since i put them on for a 25 mile ride. I love the feel. Like I said, it absorbs so much of the road imperfections. I feel like the Shimano rims/hubs are so buttery smooth. My brother has a set of ultegra rims which i had ridden on before I made the purchase and I really liked the feel. Mounting the tires was a tight squeeze. It is necessary to use some type of sealant (I used hutchinsons latex sealant) for the tires to seal and seat into the rim.
No special brake pads are required because the braking surface is not carbon. This was a huge attractor for that I wouldn't need carbon specific brake pads. That will be a fun bike, your Cervelo R3. I was going to go to a demo day 2 or 3 weekends ago to test ride one. I am running dura ace 7800 gruppo on my bike. I love the Dura Ace gear. I think you should build your bike up with a Dura Ace Di2 gruppo )) haha. As far as the wheels appearance, which is so important they look awesome. You can also get the ultegra in tubeless for much less. But that wouldnt work to build your bike up with DA gear and not get DA wheels.
Overall, an awesome wheelset. Shimano definitely makes a good wheel and I agree about having the loose bearings. I think it would be a great opportunity with building up a new bike to enter the tubeless world. Feel free to ask more questions, especially as i get more miles on the wheelset.