I also use Speedplay (X2) pedals on my road bikes, and yes, the cleats get scratched up almost immediately, especially on chip-seal roads. I use coffee shop covers when I'm going into a store or at a rest stop on gravel, but for stopping at a stop sign or whatever, yes, they are going to get scratched. That's a small negative of road shoes/cleat systems to me, as opposed to recessed cleats w/mountain shoes. The good thing is, they still function fine even if they don't look so purty.

Emily