Advice and recommendations for 18 days in Namibia

$200/day each? You dont need directions to the Youth Hostel then.
That's a very generous budget. 18 days isn't long, so rent a car. You could rent from JNB airport and head straight to Fish River Canyon, on to Ludiritz, Sesirem, etc. Or fly into WHK and rent there (if you plan to see things in the south, then a JNB rental makes sense.)
We spent 6 weeks in Namibia, 4 hitching and 2 driving. We did see a lot, and from our experience I'd say stick to Namibia. I would recommend leaving JNB straight away. You are unlikely to wish you'd had more time there, but you will wish you had more time in Namibia.

Stick to Namibia. Botswana beautiful but more expensive.
Chameleon and Wild Dog/CrazyKudu used to do small group tours but the last time I was in Namibia (Last July August) I noticed that their busses had got a lot bigger. I did trips with Chameleon in 2003, my first time in Namibia and it was a great way to get a flavour of the country as I couldn't afford to hire a car on my own.
Getting around using public transport does limit you to where you can go and you do need plenty of time and patience sitting around waiting for shared taxis to fill up.
Don't spend more than 2 days in J'Burg: Apartheid Museum is a must.

Thank you both for your valuable advice! At first I'd disregarded the option of self drive, but it might not be too bad after all. I think I'll try to make an inquiry at Namibia Tours and Safaris and see what they can come up with, thy seem very reliable. If we could have an accommodated 18 days trip including some guided game drives within our budget it would be fantastic. However, there's also the cost of fuel, but I don't know the fuel prices there – surely they can't be as high as in western Europe?

You advice regarding staying in Namibia has been noted, thank you so much, and I think that's what we'll do.

Once again thank you for your replies!

as posted above, i would not spend too much time in johannesburg, and spend the rest of your time in namibia. and i would rent a vehicle, namibia is a great country for self-driving. i would fly joburg - windhoek - joburg, and rent the vehicle in windhoek and return it there. if you do a one-way joburg - windhoek (or vice versa), you have to pay a pretty high one way rental fee.

i would look at renting a 4x4 vehicle with a rooftent (or a bushcamper). and to take a break from camping, you can treat yourselves to a night in a nice lodge in between. you dont want to camp in windhoek (and you dont need to spend a lot of time there), and you dont want to camp in swakopmund, but you can find good accommodation (b&b's) that are not expensive. you definitely want to have 2 nights at sesriem (where i would camp) and i would also include 4 nights in etosha. and this is where i would splurge and stay for 2 nights at dolomite camp, which is in the western part of the park that was not acessible for visitors for many year. apart from those "musts", depending on your interests and on how quick you like to travel, include other destinations. i would probably either include the south (fish river canyon, lüderitz, keetmanshoop etc.) and then not get further up north than etosha. or include the north and/or the caprivi strip, and then not get further south than windhoek / sossusvlei.

That's great info Nathalie, thanks! Based on the responses received here, and on our research in general, I think we have pretty much decided to do to the self drive thing from Windhoek to Windhoek. I think we would prefer to stay two nights wherever it makes sense, to take a break between the long drives. If our budget permits, we will probably do some local game drives since I guess the possibility of seeing a lot of animals is bigger when going with a professional who knows the good spots. All your other recommendations have been noted, thank you very much! :)

How about the cost of fuel, is it expensive in Namibia?

Cheers,
Soren

It was around 100,-- NS$ per L in 2012, the further away you go from Walfish Bay the more expensive it gets.

For Etosha you don't need a guided tour, when you drive around you'll see cars stopped at the road, just pull up and ask whats around.

In case you can read german look here http://www.namibia-forum.ch/forum/6-namibia.html

We used http://kalaharicarhire.com/ he rents out older cars pretty cheap, but has a good reputation, ours was pretty old but we had no issues during our trip, do spoil yourself on Dolomite it's fantastic and if you book over a travel agent it wasn't much more expensive than the other camps in Etosha, but check the NWR site first.

Thanks a lot! However, I hope the price of petrol was around 10 NAD and not 100 (app. 10 NAD to 1 dollar, no?). The Dolomite camp seems awesome, I'm afraid we to splurge a bit there :)

You're right got confused with other $

No problem. Anyway, just heard back from our tour operator that we are in contact with, who said that she hadn't included Dolomite in out schedule since it was quite expensive and since there "is more wildlife at the Anderson gate." Well, I guess we will have to take a look for ourselves then :)