For starters, the revovling-door managerial situation meant that no one with sufficient balls to save the company ever became CEO, this leads us to the root cause fairly quickly - Irving Gould. This man is basically Darth Vader and Satan's love-child; reading through the histories written about CBM it seems like he really wanted to kill the company.
Mehdi Ali and his Amiga Jr - man was that guy a real bar-steward.
AAA - was in development from '89 was it? Should have had EVERYTHING poured into that and got it to market around '91-'92 at the latest. AGA was never much more than a stopgap and a pathetic improvement over (O/E)CS given the movement in the Clone market at that time.
Constant rebranding of the same machine and selling it for nearly a decade? The A600 was meant to be the 300 - a cheaper replacement for the 500, like the C64C was to the C64, except it actually cost MORE to produce than the 500+ and offered no improvement in capability and screwed up any games that needed the numbpad. Not good for what was nothing more than a glorified games machine.
The 3000+ cancellation as has been said - though by that stage AAA should have already have been finished if CBM were to have survived.
The lack of any substantive money in R&D - ties in again with AAA.
The investment in the clone market - stepping on their own toes for very little profit - if any.
The continuation of the 8bit line - the C128(D(CR)) and C64C should never have been developed. After the debaclé of the TED series (C116/C16/+4/264/V364) they should have killed all 8bit development in favour of that 900 thingy they had in dev before the Amiga turned up. As for the C65 - doorstop anyone?
Speaking of the 900 - shouldn't have cancelled it. Server market is big, that thing could have really helped out CBM.
Basically with no one in charge, no one was really accountable for the devastating string of managerial disasters caused by Commodore simply having no direction.
As much as I hate to say it, they would have been better off with Tramiel.
P.S. Tramiel staying would of course have meant the Amiga never would have happened as it was his Atari that funded Amiga-Lorraine development since Atari had nothing of their own worth developing at the time.