This is definitely a taste thing and there seem to be a lot of conflicting opinions. Personally, I like them. I've looked through a lot of the forum pics and finally saw a set on a GenIII in person the other day. I still like them. Thus I have a brand new set sitting in a box here. They arrived from the PC store yesterday.
The side moldings look better on the Gen II Prius than on the Gen III Prius. The raked crease on the Gen III Prius (and other cars, e.g., Hondas) creates real styling issues when you try to add side moldings. If I had a Gen III Prius, I would not spend $120 to buy and add those side moldings. But if the dealer put them on for "free" (although nothing's really free), I'd probably keep them on.
Here's an idea: Keep them on for a while, until they get a few door dings in them (that would have gone in your door!). Then take them off, unless you've gotten used to them by then.