OK, firstly I can't comment on Namibia/Namaqualand, but my folks went there many years ago and the stories of huge sand-dunes is something I can't get out of my mind - I need to go at some point, it sounds amazing :)
Anyway, the rest:
Kruger National Park - you'll be able to see almost all the famous animals of southern Africa here (if you're lucky), aside from the Springbok. Oddly for being the nation's national animal, it doesn't appear in the park. But the Big Five are certainly there. I'd recomment Pretoriuskop rest camp for being reasonably priced, well located (near watering holes and easy to access from outside), and having great thatch-roofed bungalows to sleep in - something quite different!
Hluhluwe and Swaziland I went to when I was very young, but Hluhluwe is famous for its White Rhinocerous population - if you don't see them in Kruger, you're likely to see them here. However, if you're spending time in one park, Kruger tops them all for sure.
Swaziland - I don't know, it's a crazy country that still has a King with a 'Virgin Dance' of tens of thousands of young girls who dance for the King in September - a surreal society. But I prefer scenery in SA.
Cape Town - of all the expats, they almost exclusively say that if they returned to SA, they'd live in Cape Town. It's become a spectacular city, with stunning beauty with the amazing backdrop that is Table Mountain. Highly recommend both the Cable Car and the walk up to the top - look out for the very cool Dassies that live up the top - oddly, their closest relative is the elephant!
Last time I was in SA, we drove part of the Garden route east from Cape Town, and turned inland towards Oudtshoorn - famous for its ostriches - it's bizarre seeing fields and fields of them! Make sure to visit the spectacular Cango Caves while you're there, and have ostrich for dinner!
Don't forget Stellenbosch, just outside of Cape Town - if you've had South African wine, odds are it came from here. Wine tours available!
From there you can either return to the coast and keep going east along the Garden Route. It's very scenic, and my family did this trip in 1989 over a week from Durban to Cape Town. However, in 2005 I continued on through the Karoo - and that's amazing landscape, make sure to stop in the middle of absolutely nowhere once the sun has well set, and look at the stars - I'll bet you've never seen so many in your life!
The one problem with this route is there's not much all the way to the Orange Free State province, and Bloemfontein. We stopped in Kimberley to see the Big Hole. It's HUGE, but warning - it really is just a hole. It takes 5 min, and then you're done.
For completely different scenery, I'd recommend the Drakensberg mountains in Natal - any of Giant's Castle, Dragon's Peak or White Mountain. Spend three days doing amazing hikes, check out the Bushmen paintings, do some trout fishing, and soak up the scenery.
Also if you go down to Durban and the Wild Coast (although the latter is really part of the Garden Route), you'll see some of the best beaches mainland Africa has to offer. In addition, the road between Pietermaritzburg and Durban contains an area known as the 'Valley of a Thousand Hills' - part of the Zulu Kingdom, and consider that every year in May a 86ish kilometre marathon is run between these two cities! Perhaps check out a Zulu experience around here, and I can recommend the museum in Pietermartizburg.
Above all if you can be flexible, once you're there you're bound to hear ideas from others for day trips.
Cape Town to Durban along Garden Route: a week or so is doable
Drakensburg: allow 3 days to really enjoy
Cape Town to Durban inland route, we did in 5 days, although with some big driving we did it in 3 in 1989.
Note: Speed limit is 120km/hr, but most drivers tend to drive about 140km/hr, so it's amazing how quickly you can eat up the distances...