Many factors went into Commodore missing these and other opportunities.
Geography
Amiga was pretty big in Europe and even here in Australia it enjoyed a healthy following and made its way into many businesses. But in Apple's home market, the US, Commodore did't spent enough marketing $ to get Amiga into schools, and into the creative business mindset.
Socio-economic
In the '80s Apple had a strong presence in elementary, middle, and high schools. And IBM had convinced many a business to buy an XT and an AT system. American businesses liked to use American business focused brands. Commodore was seen as the games PC maker, even though they also diversified their business into UNIX and IBM compatibles. Atari would have had some similar stigma.
Sales and Marketing
IBM was a giant and despite how much money they practically handed to Microsoft, they were not going to suffer if they made a mistake here and there. The Open Computer Platform accidentally invented by IBM made it difficult for all including Apple. Apple actually spent quite a bit on marketing but they too were floundering in the late '80s and early '90s, its financial troubles softened by extended Apple II contracts and DTP stalwarts like Quark.
Industry Trends
It's not so much that IBM won, it was the open computing platform of bare motherboards that can be populated by an assortment of daughter cards. Commodore Amiga, Apple, Sun, Silicon Graphics, and even NeXT were all still thinking of a completely custom and proprietary system and bus architecture. Some even used proprietary RAM. Apple failed a little bit less than Amiga to position their higher end M68k computers using the 030 and 040.
Business Management
IBM had made mistakes as well and continues to do so today, but when you are the No 1 computer company on the planet it is justified to refer to them as "too big to fail".
Who's not too big to fail? Digital/Compaq, Sun Microsystems, Silicon Graphics (sgi), Atari, Commodore, Osborne, Wang, and even Apple who were at the brink of bankruptcy in the mid-'90s. Compaq was once rated #2 and Sun was rated #3. And if you consider the gaming hardware market then we also have Atari and SEGA.
By the end, Commodore had made too many bad calls and/or did not insulate itself enough with deals and legacy installations to make it through the continually changing ICT landscape. Not sure if having Adobe write software for the platform would have made all that much of a difference.
