It's just embarrassing. It really is.
Notes:
The Labyrinth Zone boss doesn't play the boss music, but continues to play the Labyrinth Zone music.
You can beat the Star Light Zone boss just by jumping from the seesaws. In the Genesis version, you had to use the exploding mines to beat Eggman.
When you pause during the Special Stage, the music still plays through.
The special stages seem really rushed. The mishap above is a good example. Also, the special stages jitter while they rotate. When you stay on a "Reverse" block, the rotation keeps on reversing back and forth so long as you're on the block.
A lot of sound effects are missed due to the audio playing too many effects at once. For example, you don't hear the water slide in Labyrinth Zone Act 3 move at all. Also, when you destroy an egg capsule at the end of an Act 3, you'd usually hear a lot of explosions, but in the GBA version, it's totally silent.
The physics are weird and look really ad-libbed. The seesaws in Star Light Zone are a good example. It feels more like you're walking on stairs than on a smooth slope.
Sometimes, wherever you'd get crushed in the Genesis version, you actually get moved off to the side in the GBA version.
The slowdown is embarrassing.
The sprites of the horizontal springs are flipped upside down.
The background in Scrap Brain Zone Act 2 is not animated. In the Genesis version, it is.
The sprites are
dithered.
When you die, the music doesn't restart - it just keeps on going.
The game seems really rushed from Star Light Zone on.
The Final Zone music doesn't play at the end of Scrap Brain Zone Act 2. It does in the Genesis version.
The air sound effect underwater (the "ding ding") only plays when you're running out of air.
When you start Final Zone, you don't look like you're springing up from below. You just start standing on the side. In the Genesis version, you start by springing up from below.
The underwater wavy effect that appears in the Sonic 1 JP version doesn't appear in the GBA version.
The Genesis version feels so much more natural. And its music sounds so much better than the GBA one.