FWIW, that connector is actually an AMP Universal Mate-n-Lok (Molex MAY cross it under another name, but I'm not sure that they do). They are MUCH better than the old school 0.093" pin and socket connectors (made by both Molex and AMP as well as others) that you may be used to. Rather than friction lock, these employ a set of latches that you squeeze to disconnect. The contact design also isn't subject to as much spreading upon mate/unmate and tends to last longer. They're still not designed for repeated cycling, but if all you've got to go on are those cheap 0.93" things that Rat Shack sells (and that were so popular on older games), I think you'll be pleasantly surprised at how good this particular connector is. I'm a fan of them and like to use them whenever my application allows a connector of such large size.
If you're swapping things around constantly, then yeah, use the USB connector. It *is* designed for repeated cycling. However, I'd anticipate several years of lifetime from that other connector even if you cycle it every few weeks.