I have traveled different routes. The Frankfort route is a good option but I believe that I will not be flying Air Namibia anymore. They do not have enough airplanes that are capable of flying to Europe, and consequently cancel too many flights for my comfort. I think they bought a second long distance airplane, but they used to have only one. I get an uneasy feeling when the PH calls the airline on the day of departure to see if they are "flying today".
Johannesburg airport can be a big pain but that is the way I go now. I stop off at Africa Sky guesthouse for some rest and good food before continuing my journey to Namibia, Botswana, etc. Travel is often very tiring and I do not like to start a hunt jetlagged.
