I left the stock ones one and for the trails I ride i didnt have a problem with them until i went riding in the coal mines and came home with a bent rotor from the rocky area. I went through a set of pads till i realized the rotor was bent and i could see on the plastic skid plate where it hit the rotor. Now I have a prm skid plate (.250) under the swingarm and it has kept them mean rocks away from the rotor.
I think aluminum skids are a necessity - better to spend some money now than a lot later on a bent a-arm, dented frame or smashed swing arm/busted rear shock/busted rear rotor.
But it really depends on how heavy you are, where you ride and how you ride. Aluminum skid plates probably aren't necessary if you are only ever going to ride on sand (((edit))) although the sand will work away the paint on the underside of the quad over time, so skid plates might even be helpful there too.