If your looking for bad reports, you will find them.
Both should be good. Far less reliable bikes have been used...
To watch for in the BMW:
- waterpump is made of plastic and seems to go with a lot of bike around 50K KMs. Changing it is easy, except for accessing it. There's a solid oil feedline right in front of the engine casing that you need to remove. So changing the oil line for a flexible one should sort that.
- get new filling on the seat
- steering head bearings are easy to go on an F650. Make sure they are in top shape before leaving
Check
The BMW F650 Technical FAQs for further info
To watch for with the Africa Twin:
- fuel pump (chang it for a Mikuni vacuum or Facet)
- regulator/rectifier: change it for a modern MOSFET type, or at least bring a spare and check the connectors and wiring. Bad contacts ruin the R/R
- get new filling on the seat
- make sure the chain has the right amount of slack and the sprockets make a good fit. Otherwise you'll ruin the outgoing shaft and bearing. Not something to repair in the middle of Africa
and for both:
- stock shocks and springs are, well... not the best. Too light for overlanding fully laden. Not undoable though, plenty of people have done so. But most who have changed for proper springs/shocks are very satisfied. Makes your ride more comfy and better handling bike.
- bearings and seals. Make sure they are in good shape before you set of.
Me, myself am using a Twin to ride Africa, but have ridden the F650 in South Africa before. Liked it because its a small bike, though relativly heavy. Very good on fuel economy if you be easy on the throttle. Seats on both bikes are shit though