The unfortunate thing is that your "insides" idea won't happen unless Sony goes and reprograms all of the games. Even with the improvement algorithms they had, it didn't work with 100% of the titles... so trying to get more creative with tricks like that would make the compatibility rate drop even more.
Basically all I'd really think of right off the bat would be to redesign the thing to not have a slide-tray for the CDs; just make it a flip-top... oh and possibly curving some plastic on the inside so that it doesn't absorb as much dust as it seems to do now.
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