Hi Sam
Just caught up with all your travel experiences. I did a similar route to you last year and reading about you is making me decidedly itchy-footed again.
Just read that you were unsure of which route to take in Africa. I did an overland tour from Cape Town to Victoria Falls and would certainly recommend it. I never went further north than Zimbabwe so can't comment on that bit, but Botswana in particular was one of the most amazing experiences I have had. As part of the tour we did a three-day bush camp in the Okavango Delta, traveling by makoro (canoe) with local guides to a remote area where we went on sunrise and sunset game walks through the bush with a tracker. It certainly beat any of the game-park experiences I had. Also, Cape Town is one of the most beautiful cities I have been to (and amazingly cheap due to the exchange rate). Admittedly it is very touristy, but much more cosmopolitan than east coast Australia. Also, if it's your thing, you can visit Stellenbosch and stock up on some excellent, very cheap wines for the trip home!
Whatever you decide, have an amazing time (I have no doubt you will!)