Hm. Looking at Metroid 2k2's forums...
"I've noticed several differences in MP3 so far.
When you choose to have the hint system disabled, the AU continues to upload coordinates to you but it doesn't take you to the map screen immediately afterwards. For some reason it did go to the map screen when the norion generator coordinates were uploaded, but everytime since then it has not.
The 90 degree corridor near the save room on the way to to the metroid lab in Elysia used to have jolly roger drones in it, now it has an endless stream of puffers. (It's the corridor that you have to use grapple lasso to pull a coouple of blocks out and then screw attack over to a missile expansion)
The rotating cage in Elysia has been replaced by force fields which flicker on and off at regular intervals.
ALSO - the security station in Elysia used to have metal debris blocking the lock, requiring you to melt them away with plasma first."