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I found out this:
http://community.eu.playstation.com/t5/PlayStation-3-Technical-Help/Uncharted-3-stuttering-New-Super-Slim-500gb/td-p/17801296/page/3

apparently the Hitachi HDD in super slim, sux:
"The Z5K500 suffers considerably when it comes to performance, however; its read performance is middle of the pack but its write performance is downright awful. Furthermore it has a high average write latency, which hurts performance across the board."
Because games like uncharted are writing to the HDD almost all the time, it suffers from the above issue.