It's a tough one. I do love playing the hindsight game; He who fails to learn from history is doomed to repeat it.
At the time I remember being happy that Atari didn't have the winning bid, but that was because I was a C64 user and was not interested in switching camps, and we'll never know how the industry might have turned out if it did.
Jay Miner and Co. set out to created the most advanced gaming computer, so it made sense for Commodore as the C64 was the most celebrated gaming computer of the early '80s. If Commodore wanted to continue playing (pardon the pun) in this market space, the Amiga architecture was surely up the the challenge.
But the Commodore of the second half '80s was more interested in playing with the big boys, fancied itself in competition with IBM and HP. And with money being tight they did what pretty much many businesses and individuals end up doing; they rationalised.
I wasn't there but I could imagine conversations along the lines of:
"Well we cant afford both an advanced gaming computer and an advanced Unix business machine".
"The C900 is not really designed for gaming and it would cost too much as a family computer"
"The Amiga architecture is powerful enough to also be used as a business machine"
I would have to say that Commodore would have been better off going with the high end business and education market. Who knows, they might have even survived throughout the '90s and eventually got bought out like DEC, Compaq, or Sun.
As for the Amiga? Through another funding source it may have also survived, but I'd have to venture that somewhere in the first half of the '90s it would have become a games console, competing with Nintendo and Sega. And maybe today I would be playing the latest iteration in the Alien Breed saga on my 2012 Amiga X1 console in 1080p 60fps glory with dozens of other players online via AmiNet.