Mega Turrican has twice as many colours and better gameplay.
The underwater boss moves different and is harder.
The gliders above the scrapyard don't move in the Amiga version. They do move in Mega Turrican (making this part way more interesting and challenging).
The first boss of the final world (the two guns moving in a circle) is broken on the Amiga: you can stand on the right side of the middle platform without ever being hit by the cannons' shots - on the Mega Drive there is no such safe spot thus making the boss more challenging.
Also the walker boss in the final world is easier in Turrican 3.
Only the music and sound fx are (a lot) better in Turrican 3.
Conclusion: Mega Turrican is the better game.
In comparison Turrican 3 feels like a beta-version.
The perfect version of this game would be Mega Turrican with Turrican 3's sound.