Perfect, love talking about rim design.
My ideal wheelset:
Let start with the general shape of the rim profiles. Elilptical like the scope rims in the attachment. This is critical in the front rim. This profile provides a great balance of speed and stability and is used by dt swiss/swiss side who make very fast wheels as well as specialised on their very fast roval rapide clx II, though scope claim theirs are even faster. The idea is that the cross section of the tire and rim combined forms an ellipse. It works well both when the airflow hits it for the first time and the tire is the leading edge and rim the trailing edge and when it hits it a second time when the rim is the leading edge and the tire the trailing edge. A V shape does the first well, but absolutelly terrible at the second.
Hubs and spokes:
Obviously deep aero carbon spokes. The hub interface should be something similar to farsports, scope, crw, etc. Basically replicating a regular straight pull hub but with carbon spokes. This is safer because the spokes wont pop out in case of rapid tension loss, lighter and smaller so more aero. H-works make great hubs like these and aparently dt swiss are moving into this area as well. The spoke to rim interface should have an external nipple like the new superteam wheels, so its possible to true the wheel from the outside with a mounted tire. This makes servicing easier and allows you to true more accurately. It also means you don't need spoke access holes in the rim bed so no need for rim tape. Ideally you would have as much of the nipple still hidden, showing just enough to be able to work on them.
Front wheel:
50-55 mm deep, from the development white papers I've seen, 50 mm is around when a wheel can start taking advantage of the sailing effect at higher yaws. 21-22 mm internal width and 30-31 mm external width at the rim edge. That way you can put 25 or 28c tires on without them balooning beyond their labeled size and they will stay narrower than the rim giving the best chance to form the aforementioned ellipse. As low a spoke count as is feasible to reduce weight and improve aerodynamics. Stiffness isn't as critical in the front as it is in the back.
Rear wheel:
60-70 mm deep, 24mm internal width and 34-35 mm external width. This one is way wider because the air is so messed up by the time it gets to the rear tire that width matters a lot less for aerodynamics as their biggest impact is when providing a sailing thrust effect in crosswinds. Therefore we can mount a wider tire for improved comfort, rolling resistance and puncture protection. Elliptical shape is probably still ideal but less critical as the first time air will hit the tire is at the seat tube where airflow is all kinds of messed up, so optimising the design for when the air hits it the second time could be more beneficial. Tire should still be notably narrower than the rim. Spoke count should be higher, probably 20-24 spokes. Ratchet hubs with dt swiss compatible internals.
Obviously everything should be as light as possible
Edit: also no wavy rims, their only benefit is better cross wind stability by reducing the stall angle of the wheel i.e. the airflow is so messed up that it doesn't even push the rim anymore, meaning you lose the sailing effect. This is unneccessay with good eliptical profiles because they can enable the flow to have a smooth transition from one side to the other.