go to homedepot and pick up a tin bottle of brasso metal polish ($4). put a drop of it on a lint free cloth and polish your game disc until it shines, focus on visible large scratches. try to play the game, and if still skips, do it again.
my MGS3:Subsistence disc was all messed up by my PS2 and would crash or would say disc error during cut scenes, after polishing a couple of times in different places, i was able to play all the way through.
this is a known solution for repairing discs, works very very well. I was almost ready to buy a new copy of MGS3, until i tried the Brasso Metal Polish.