In terms of using a 2000 case on a 3000, I'd be wary. While the systems are very similar, I'd be concerned that critical aspects had changed in relation to screw points, the UMD drive mechanism, and perhaps the speakers. Thats just a word of caution -- outside of plugging up the microphone, there may be no problems whatsoever.
But with that said, I had a PSP 1000 which disappeared. When it came to replacing it, I went with a gently used PSP 2000 over a 3000. For me, I abhor the new 3000 screen. Some people may not have any problems with it, but the interlacing drives me nuts. Unfortunately, this is a hardware issue that can not be repaired with a firmware update -- so either you like seeing images torn apart at the scanline, or you loathe it.
Otherwise, the 3000's new screen has some tweaks that a person can configure to make it prettier in daylight.