Changes:
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Graphics:
1: Brighter and lower resolution to fit the GBA screen
2: Touch fuzzy effect is more jagged and not present in the farthest background
3: Some of the rock-textured platforms scroll vertically more choppily (as does one of the lava effects). Strangely this problem is only present in one of the platforms and lavas. Only a couple of levels have this strange issue (probably just lazy programming on Nintendo's part).
4: The stomach of the frog boss doesn't have a wave effect anymore.
5: The ending sequence with the stork is choppier and slower.
6: The spell effect where Kamek transforms the boss in the beginning of a battle doesn't have the colored transparent curtain that used to pore over the screen like a liquid. He just drops some sparkling dust over the screen. Strangely, the effect is still seen when you beat the boss and multicolored spheres bloom out of the boss. I guess another lazy programming error.
There are probably some other things lost in translation graphically, but the art style and most of the primary effects remain intact. I only did this deep of an analysis because I used an emulator to view them side by side. Most people will pay no heed to the changes (I myself forgive them because of a great game.
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Sound:
1 Yoshi now has his "Yoshi's Story" voice and some other sound effects have been added from that game too.
2: Slight GBAifying of the music. They didn't really butcher it much, and it's still good and catchy.
3: Old sound effects have also been toned down a bit. Kamek has a heavily altered version of his old voice and it sounds like it's being played through a badly tuned radio underwater. Mario has a different (but no less obnoxious) cry.
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Yoshi's Island Advance is still the same game and people who have played it a long time ago will notice the alterations much less than people fresh off the SNES version. A game I highly recommend and a great portable game with a long lifespan. I give the SNES version a 10/10 and the GBA version a 9.5/10. It retains the same gameplay with some cut corners in GFX/sound, and it's PORTABLE!