You can fit a lot into two weeks, but it’ll take a fair bit of driving. Here are three options to consider.
To see the most in a short time, first drive from Windhoek to Sossusvlei and spend a few nights there before heading northwest to the coast. Stop in Homeb or Blutkuppe campsite on the way to Swakopmund and then take a couple of days to explore the area, visiting the nearby ‘Moon Landscape’ and welwitschia fields. If you have a 4×4 you could also book a guided day trip into the dunes around Sandwich Harbour. From there, drive north along the southern Skeleton Coast, but turn inland for a few nights at Spitzkoppe. With a 4×4 you can then drive through the spectacular Messum Crater and spend a night or two at Ugab River Rhino Camp. It’s a six-hour drive from the Ugab River to Okaukuejo Camp for a final few nights in Etosha National Park.
The best two-week wildlife route is from Windhoek to Etosha, then northeast to the Zambezi Region. Spend four or five days in Etosha, and the rest along the Zambezi. Even if you don’t like fishing – one of the main attractions of the area – try and get out on the water to see the elephant, hippo and crocodiles up close.
For a landscape-focussed, two-week trip, you can head south from Windhoek and make your way slowly to the South African border. Stop in the Namib-Naukluft National Park and then spend a few days in Sossusvlei. Continue south through the NamibRand Nature Reserve and if you have a 4×4, take the D707 loop which has particularly beautiful views. Spend the last week along the eastern edge of the Fish River Canyon with stops at Hobas, Ai-Ais and along the Orange River.