A topic near to my heart as I'm preparing for a trans-Africa trip (thanks for the info on the sprocket btw). Here's a handfull of problems I have found with the DAKAR. Most have been external/body type issues.
1. Indicators are inflexible and will break in any crash. Replace with soft ones (or make something custom, I have replaced the rear ones with Land Rover tailights. I have pics if anyone is interested.)
2. Taillight/license plate assembly is weak. Will break and cause trouble off on bumpy roads. I replaced this when I replaced the rear indicator lights. Throw away that plastic mudguard thing too before it breaks and goes through your spokes.
3. Gear/brake pedals weak and exposed. They stick too far out, and for some reason known best to BMW, the gear pedal isn't hinged (standard feature on MX and Enduro bikes). I straightened my brake pedal, but am at a loss about the gear pedal...carry another one as a spare?
4. Definately do not buy the BMW expandable pannier boxes. Plastic mounts, rattling, not at all waterproof, and sure to be destroyed in even slow tumbles.
5. No dust boots on forks means easily damaged seals equals leaky forks. Mine are leaking already (12,000 km) and I plan to add boots when I replace the seals.
6. Another BMW oversight: No guard on the radiator. Some make their own out of wire mesh, some buy Touratech. I was surprised how many little rocks dented my radiator before I added a guard.
It occurs to me that this might all be obvious...oh well!