I've got a bit of experience with both options; we stayed at Cape Town and while there did an overnight to Kruger (yes, pretty insane thing to do, but somehow worked out nicely). On the way to Kruger we flew direct from Cape Town to Nelspruit on SAA's direct flight. It's not cheap ($250 one way per person), but it gets you into Nelspruit just past noon, with just a short 45 minute drive into Kruger.

On the way back, Nelspruit flights didn't work out, plus there was the expense, so we did the transfer to JNB. Took the 8:15pm flight JNB-CPT on Safair. Very reasonable at about $60 each. You *will* get tagged with luggage fees though, but they're not predatory or hidden. Check their website for details. If you can avoid that long drive to JNB from Kruger, do so. As others have said, it's not terribly interesting, and you're going to be pretty burned out by the end of your safari if the weather is warm.

Also, since he's a photographer, he may have seen advice from others saying you don't need a long lens at Kruger. Well, that depends. There are certainly many opportunities for mid-zooms, but I would not have gotten decent photos of big cats and rhinos if I'd left my 150-600 at home. That's with a Canon 1.6 crop factor body.

Hope this helps-