Since I chose a simplified visual style, my biggest headache has been the design of antibodies - too realistic, and they look confusing and cluttered, too simple and they don't really communicate enough information.
My first problem was how to produce a design for the antigen-antibody receptors that would work in 3D and convey the idea of matching pairs. Although male-female docking shapes work well in 2D, I believe that the best option is to use colour to indicate the pairs.
The second problem was the design of the body of the antibodies - although the forked design is scientifically accurate, it creates quite a lot of visual clutter. On balance, I fell that "single receptor" antibodies are cleaner, so I'm going with that approach.