Choosing the right wheel depth is a part of the bike building process that causes confusion for many. The fastest combination of wheels is a disk in the rear and a tri-spoke wheel in the front. In this context "fastest" means most aerodynamic, however this combination results in a really stiff ride, and a lot of side force in a cross wind. The fastest combination of wheels makes no difference if you are not in an "aero" position. The increase of side force on the front wheel in a cross wind will affect the handling of the bike, if you are an inexperienced rider, a light rider, or a nervous rider this added force will cause the front wheel to be more likely to be blown around and have you leaving the aero position for a better feeling of control.

In general the shallower wheel will be lighter, easier to handle in a cross wind, but less aerodynamically efficient. Some riders choose to "mismatch" their wheels (think 88mm in the rear and 60mm in the front) to provide an aerodynamic advantage all while providing a technology package that the rider feels comfortable with. A shallower wheels tends to be less stiff than a deeper wheel, on a course with lots of bumps this can have a drastic effect as to how you feel entering T2. If a course is very hilly a shallower wheel will save you weight and effort when climbing. If a course is flat and fast then a deeper wheel with a slight weight penalty will save you time. One last thing to consider is the amount of turning in a race. If you have a lot of turns a heavier (deeper) wheel will take more torque to get back to speed and over the course this can leave the legs in a pretty rough spot to run on.