Hi Jools,
Like the others I've done South Africa with the Zambia add-on - in Sept 2011 and it was the best holiday of my life! The itinerary has changed quite a bit since then, but it still looks very good. The beautiful scenery around Cape Town and the excitement of the game drives are the highlights and Zambia was the icing on the cake, especially the chopper ride over the Falls, the sunset cruise on the Zambezi and the day trip to Chobe National Park in Botswana, all of which you can still do on this tour, as far as I am aware.
Having said all that, I have been hoping for several years that JY would introduce Namibia and to my absolute delight they have and it looks like a brilliant itinerary! I've booked for next May and it looks like places are filling fast, certainly on the Feb and May departures. May looks like a really good time to go, with the temperatures not being so high and low humidity. The unique landscape featuring the highest sand dunes in the world, coupled with an insight into local culture and game drives in Etosha should make it an amazing holiday.
So I reckon whichever you choose you will have a brilliant time; I would however echo Sally in that although Namibia seems to be selling well, it mightn't be on the JY tour list indefinitely; whereas S Africa seems to come up in one format or another every year. So if I were you, I'd study both itineraries very carefully and go for the one that appeals the most - and Julia will answer any queries you have. Go for it!
Cheers,
Bob