Game companies make their money on software, not consoles, so I am sure you will see many topics pop up upon release of the Wii and PS3 with complaints about games getting scratched. I am not saying that it will all be the systems fault but with slot loaders you have to handle the game disks much more than tray or lid systems.
Personally, I like the lid method as I have never scratched up one PS1, Dreamcast, PS2 (on the slim system) or Gamecube game with the way the disks lock into place not really touching anything.
Moving to slot loading probably has to do with piracy as it will be a little harder to trick the system but I am sure you will see mod chips and what not by Christmas time.