I've seen a softopper first hand, but haven't seen a supertop. I personally don't like the criss cross supports that the softopper has and the velcro'd rear flap will eventually remove itself from your tailgate. The ability to flip it up though is pretty sweet.
I had a can-back on my ext. cab taco. It isn't too difficult to remove, as I always left the rails connected to the truck and just unscrewed the uprights. My truck was totalled and I liked the can-back so much (and not easy to get these days) that i'm saving it under my bed until I get another truck.
The ability to mount a rack directly to the can-back is also a key feature. Whether it's an RTT, kayaks, basket, or lumber, the can-back holds them solidly.
Used can-backs come up every now and then, a perfect black one on ttora last month for $400. Sorry to skirt your question comparing the two, but I would wait if I were you.