Two weeks is just enough time to do the classic Botswana circuit and see the pans, the Central Kalahari, Moremi and Chobe.
From Johannesburg, you can drive into Botswana from the southeast and stop over at Khama Rhino Sanctuary before heading up to Lekhubu Island. From there, either cross the Makgadikgadi Pans if they’re dry or detour around them via Nata. Spend a few nights in Nxai Pan National Park and a couple more in the Makgadikgadi or Central Kalahari. Stock up in Maun and you’ll then have a week to see Moremi and Chobe, before the two-day drive back from Kasane to Johannesburg. Two weeks is stretching this itinerary. 15 or 16 days would be ideal.
If you’re flying into Maun, follow more-or-less exactly the same route, but start with Moremi and skip Khama Rhino Sanctuary. Use an extra day in Maun to take a helicopter flight over the delta, or book a night with Xomae Group on their wild Moremi island camp, Gadikwe 1.
Another two-week option is to drive south from Maun towards the Kgalagadi. There’s a sandy, but fun 4x4 trail through the Mabuasehube Game Reserve to Kaa Gate and from there you can drive northeast to Khutse Game Reserve and the Central Kalahari. These areas are best from March to May and you can round off your journey on the Makgadikgadi and Nxai Pans, both of which should still have abundant wildlife.