To be honest, while I think it was a bad decision for Commodore not to jump at the chance to have an Amiga in Star Trek, I have to wonder how much difference it would have made in the long run.
Put it this way: How much of Apple's current success do you think can be attributed to having a Mac II in Star Trek? Not much really. It may have caused a boom in sales of Mac IIs at the time, but Apple still ended up in financial trouble despite this, and had to be bailed out. Apple are successful now because their products are good and are marketed well, not because one of the products was in Star Trek once.
So how much difference would it have made if an Amiga had been on Star Trek instead? In my opinion none, unless the decision to do this would have spurred Commodore on to market their products better, and maybe not make some of the bad decisions they made.
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moto