Cubase was better than any amiga sequencer. Hardwarewise the Amiga was superior to the ST, but I don't think MIDI was only the only way for the ST being so popular. Atari had this magic B/W monitor that suited more to business software. Mo surprises why business software appeared more to the ST back then. The Amiga went up in terms of business software after 1991-92.
Another aspect that ST was preferred by people, was that it was much easier to do programming with it. Let's face it, we are talking about 198X! ST was much easier to do programming simply because you knew where you were standing. I used to love playing with assembly back then and I can assure you that when I moved to the Amiga, I was lost. What you could do on the ST on your own, you needed 2-3 people to do it on the Amiga. That's why most Amiga games were ST convertions. I believe that the Amiga was explored to full depth, 8-9 years after it was released. Same goes for the STE and Atari Falcon. STE and Falcons were great machines that were probably never explored to full depth. I tried to do some programming to Falcon once, and I almost smashed it! Too difficult. DSP here, blitter there, well known limitations in the hardware etc...
I agree that the Amiga hardware was superior and it was not just piracy that sold STs (after all, Amiga pirates made piracy a science