1. Cape Town
All the accounts I've been given is that Cape Town is THE place to visit when in South Africa. But it involved an extra flight and an extra 4-5 days we just didn't have.
2. Namibia - particularly Hiking the Fish River Canyon
3. The Gorillas of Rwanda - you can see the gorillas from Uganda or The Congo as well, but we heard great things from those who had visited via Kigali
Of course that's still not everything Africa has to offer!
Looking back at things it would have probably been smarter to do Rwanda this trip and leave Botswana for when a trip to Namibia is planned, but that's one of the great things about travel, each trip you learn!